Clone Wars / Legends The Clone Wars ( 22 – 19 BBY ) , also known as the Clone War and the Great Clone War , was the name given to the major galactic conflict fought between the Galactic Republic and the Confederacy of Independent Systems . The war was named after the clone troopers utilized by the Republic against the battle droid forces of the Separatists . These armies , the Grand Army of the Republic and the Separatist Droid Army , were two of the largest ever pitted against each other in galactic history , and the fighting between them rapidly spread to countless inhabited worlds . Beginning with the First Battle of Geonosis , both sides scored significant victories over the other , and at different times during the war either seemed likely to triumph . The first two years of the war saw both sides skirmish with and raid each other , while fighting a handful of significant battles and trying to gain allies while they built up their respective war industries . A series of Republic defeats in the war ' s second year culminated in Operation Durge ' s Lance , a major strike into the Core Worlds led by the Supreme Commander of the Droid Armies , General Grievous . After the defeat of Grievous ' forces in the Core , however , the Republic gained traction when it mobilized its greater industrial base . Using superior numbers , the Republic drove Separatists from the Core and Colonies and engaged them in their own territories , a series of attritional campaigns known as the Outer Rim Sieges . In an effort to reverse the course of the war , Grievous launched a massive strike on Coruscant through the Deep Core . Much of the Confederate fleet was lost and their Head of State Count Dooku was killed over Coruscant . General Grievous was subsequently killed at the Battle of Utapau . This , coupled with the issuing of Order 66 and the deactivation of the droid army , brought an end to the fighting . At the time , it was the largest galactic conflict to date . Unbeknownst to most of those involved , the conflict was started , maintained , and eventually ended by the Dark Lord of the Sith Darth Sidious , whose ultimate goal was the transformation of the Republic into the Galactic Empire with him as Emperor as well as the eradication of the Jedi Order through the Great Jedi Purge . The conflict led to the Order of the Sith Lords controlling the dominant galactic government . Origins . Tensions in the Rim . Although the Clone Wars officially began in 22 BBY at the Battle of Geonosis , their origins could be found over a century earlier . Though a fictive event controlled by Darth Sidious , the war had its origins in the age - old divide between the galaxy ' s inner and outer systems . In 124 BBY , the Galactic Senate passed two critical pieces of legislation : the entire Outer Rim Territories were declared a Free Trade Zone , repealing numerous sector - level taxes . Since the Ruusan Reformation s of 1000 BBY and the abolition of a centralized Republic Navy , the Outer Rim had been plagued by piracy and slavers , breeding political isolation . The act hoped to jump - start legitimate commerce and so restore ties between the Core and the Rim . Additionally , the status of " functional constituencies " was extended to include Senatorial representation of the galaxy ' s largest guild s and corporations . These twin acts benefited various mega - corporations , including the InterGalactic Banking Clan and the Corporate Alliance , but none more so than the Trade Federation , a Neimoidian trade cartel . The Trade Federation rapidly expanded into the Outer Rim , stifled competition , and enforced deals with its powerful Trade Defense Force . By 67 BBY it enjoyed full voting privileges in the Galactic Senate , and within a decade commanded the votes of hundreds of systems . Many on Coruscant supported the Trade Federation , admiring the TDF ' s rapid extinction of piracy on the major hyperlane s . Others bemoaned Trade Federation corruption and the extinction of representation for the systems it controlled . The issue of the Outer Rim polarized the Senate . By 52 BBY , a faction known as the Militarist s had emerged on Coruscant , calling for the restoration of the centralized Republic Military to restore order on the Rim . Meanwhile , a terrorist group known as the Nebula Front declared its intention to fight the Trade Federation by any means necessary . Amid this political storm began the career of one Senator Palpatine of Naboo , representing the Chommell sector . Unbeknownst to all at the time and unclear to the rest of the galaxy until many decades later , Palpatine was in fact Darth Sidious , apprentice to the Dark Lord of the Sith Darth Plagueis . Over the next two decades , he would manipulate the tensions between the Core and the Rim and the government and the Trade Federation to finally fulfill Darth Bane ' s Grand Plan , a thousand - year scheme by the Order of the Sith Lords to foment a war that would destroy the Republic . As Sidious , he fomented the Stark Hyperspace War of 46 BBY , a ruse cooked up by him , the Federation , and Iaco Stark so that the Trade Federation could demand additional rights to increase protection on its ships . As Palpatine , he worked his way into Supreme Chancellor Finis Valorum ' s confidence as an opponent of the Trade Federation . In 33 BBY , he encouraged Valorum to restore taxation on the Outer Rim trade routes in order to break the Trade Federation ' s power . In exchange , Valorum offered the Neimoidians the right to unlimited defense of their merchant ships . However , the attack on their finances through taxation drove the Trade Federation , the IG Banking Clan , and the Corporate Alliance together . After a disastrous summit on Eriadu that saw four Federation board members murdered at Sidious ' behest , Nute Gunray was elevated to the position of Trade Federation Viceroy . With the Trade Federation radicalized and Baktoid Armor Workshop and Haor Chall Engineering filling its ever - larger orders for a new Droid Army , Darth Sidious approached Gunray and encouraged him to make a stand that would force the Senate to back down over the taxation of trade routes . The Battle of Naboo . At Sidious ' behest , the Trade Federation began a blockade of Palpatine ' s homeworld of Naboo . The entire incident made Valorum look weak , and in the Senate debate over what action to take over the blockade , Palpatine induced the enraged Queen Padmé Amidala of Naboo to demand a Vote of No Confidence in his leadership . In the aftermath , a strong sympathy vote for Naboo rode Senator Palpatine to the office of Supreme Chancellor . Thus , a Sith Lord had control of the Galactic Republic . The invasion of Naboo saw the continued existence of the Sith exposed to the Jedi Order after Sidious ' apprentice Darth Maul killed Jedi Master Qui - Gon Jinn during the liberation of the planet . Additionally , events during the escape of Queen Amidala from Naboo to Coruscant saw the discovery of Anakin Skywalker on Tatooine , whom Qui - Gon had believed to be the Chosen One , the prophesied being who would bring balance to the Force . With Qui - Gon ' s death , Anakin was apprenticed to Jedi Knight Obi - Wan Kenobi . As Chancellor , Palpatine promised to bring an end to the corruption that had so often plagued the Galactic Senate . The first few years of his tenure saw very little done to fulfill that promise , however . The demilitarization of the Trade Federation was viewed by many as little more than a slap on the wrist , and Nute Gunray , Viceroy of the Trade Federation , managed to avoid any serious charges against him for his role in the Naboo conflict despite opposition from Padmé Amidala . The Formation of the Confederacy . During this time , Palpatine , in his alter ego Darth Sidious , had contacted the experienced Jedi Master Count Dooku . Having lost his apprentice Darth Maul during the Naboo conflict , Palpatine was in need of a new apprentice and Dooku , whose own faith in the Republic had been shattered following the Battle of Galidraan and the subsequent inaction over Naboo , seemed the perfect one to mold . Having killed his old friend Jedi Master Sifo - Dyas to seal his fate and become Darth Tyranus , Dooku was then ordered to eliminate any reference to Kamino from the Jedi Archives : having had a vision that war was imminent , Sifo - Dyas had contacted the Kaminoans to organise the creation of a clone army for the Republic . Sidious did not intend to have the Jedi discover the clone army secretly being grown for them until they were desperate for an army . After being deemed worthy , Jango Fett was commissioned by Dooku to be the template for this army . While the future Grand Army of the Republic was being prepared on Kamino , however , other forces of clone warriors were already active in the galaxy . Cloners and their products were no secret to Jedi like Obi - Wan Kenobi and fringers like former gunrunner Dexter Jettster , and around the time that Outbound Flight was destroyed in 27 BBY , the Galactic Republic ' s military forces were engaged in combat with clone warriors , rendered dangerously unstable and prone to clone madness by being very rapidly grown to maturity . Veterans of these campaigns , such as the future Grand Admiral Gilad Pellaeon , would later consider these campaigns as the start of the Clone Wars , but to most people , they were probably only a symptom of the unrest in the Republic at the time . In 24 BBY , Palpatine ' s eight year term as Supreme Chancellor was coming to an end . At roughly the same time , Dooku emerged on Raxus Prime . In the Raxus Address , Dooku declared his disillusionment with the Republic and his intention to form the Confederacy of Independent Systems , a group of disenfranchised organizations and governments whose goal was to secede from the Republic . The Raxus Address triggered a wave of secessions , beginning the Separatist Crisis . Fearing instability amid the crisis , the Senate permitted Supreme Chancellor Palpatine to stay in office longer than the term limits the Galactic Constitution permitted . Over the next two years , many systems left the Republic to join the Confederacy , including Geonosis and the Elrood , Danjar , Tantra and Sluis sectors , bringing most of the Rimward leg of the Rimma Trade Route under the control of the Confederacy . From the beginning the Separatists ' territory was highly dispersed , dominated by a pocket in the New Territories based around Muunilinst , the southern Rimma , a pocket stretching Coreward down the Perlemian Trade Route from the Tion Cluster , and an enclave on the Corellian Run stretching from the Allanteen system to Mon Gazza . The wave of secessions intensified after the disastrous Battle of Antar 4 , where the Republic suffered a humiliating early defeat trying to overthrow a Separatist - affiliated insurgent government , and had to resort to heavy - handed tactics that harmed many Gotals to put down the insurrection . Later , these systems would be joined by the corporate entities of the galaxy : the Baktoid Armor Workshop , the Commerce Guild , the Corporate Alliance , the Techno Union , the InterGalactic Banking Clan and of course the Trade Federation . These corporations were leaving the Republic over trade route taxation and seeking their own business - friendly government . Other seceding systems simply wanted independence and were wary of forming a new centralised government . In time , the military and economic power of the megacorporations would see them as members of the Separatist Council and override the authority of the democratic Separatist Parliament . Allies of the Confederacy . Count Dooku , prevented from openly taking his own apprentice by the Rule of Two , nonetheless sought out several Force - sensitives to act as Dark Acolyte s . These individuals included Asajj Ventress , Sev ' rance Tann , Sora Bulq , Tol Skorr , Kadrian Sey , Artel Darc , Karoc , Vinoc , Saato , Trenox , and even Jedi Master Quinlan Vos for a time . All of them , with the exception of Ventress and Vos , were killed during the course of the war . In addition to this group of Dark Jedi , he recruited the Chistori warrior Cydon Prax and the Gen ' Dai bounty hunter Durge . Durge gladly joined the Confederacy , if for no other reason than to eliminate the Republic ' s army of clone troopers bred from the DNA of Mandalorian Jango Fett , as Durge hated Mandalorians . The most important and the most famous ally recruited to the Confederate cause was the Kaleesh warrior Qymaen jai Sheelal , whose body was horribly maimed in a shuttle crash arranged , though not known to Sheelal , by Dooku himself . His broken body was taken to Geonosis where he was offered a new life and the help of the InterGalactic Banking Clan for his people by the InterGalactic Banking Clan Chairman San Hill . All the Kaleesh had to do in exchange was lead the Confederacy Droid Army against the Republic who had wronged his people . Sheelal took the opportunity afforded to him , merged with his new droid body and he became the feared General Grievous , Supreme Commander of the Droid Armies . The road to war . Coruscant found itself the target of many terrorist attacks . As violence became an increasing part of the Separatist movement , the Galactic Senate debated passing a Military Creation Act that would allow the Supreme Chancellor to re - establish a centralized Republic Military . Not all were content to wait : the Judicial Forces Captain Zozridor Slayke mutinied , and with his crew established a private army to combat Separatist forces in the Sluis sector . Slayke ' s " Sons and Daughters of Freedom " won a series of victories , and embarrassed the Jedi Order after they defeated the Jedi Knight Nejaa Halcyon , sent to rein them in , and captured his flagship . A bomb explosion on Coruscant in the final weeks leading up to the war was aimed to take the life of the Naboo Senator Padmé Amidala ( ordered by Dooku and Viceroy Gunray and carried out by Jango Fett and Zam Wesell ) upon her return to vote on the Military Creation Act . After a second attack on Amidala ' s life , the Jedi Council selected Obi - Wan Kenobi to investigate who was behind the attempted assassinations on the Senator , while Anakin Skywalker escorted Senator Amidala back to Naboo . Kenobi ' s search took him to Kamino , where he discovered the clone army , by this time numbering two hundred thousand units with a million already in production . He also met Jango Fett , who attempted to escape with his son to Geonosis , but was followed by Kenobi . Kenobi discovered that the Separatists and its many corporate entities were constructing a massive droid army to wage war on the defenseless Republic . Obi - wan managed to send a message to the Jedi Council , but was captured . On Tatooine , Skywalker was ordered by Mace Windu to stay where he was and protect Amidala . Amidala , however , decided to travel to Geonosis to rescue Kenobi . Skywalker and Amidala were then captured as well and they , along with Kenobi , were , by order of Archduke Poggle the Lesser ( who was revealed to be another prominent Separatist leader ) sentenced to be executed . With the knowledge of the Separatist Army , the Senate , at behest of Representative Jar Jar Binks , himself manipulated by Vice Chair Mas Amedda , gave Chancellor Palpatine emergency dictatorial powers . The Chancellor legalized the creation of the clone army to serve in the Grand Army of the Republic . History . The Battle of Geonosis . The Battle of Geonosis was the first battle of the Clone Wars . The battle occurred after Separatist forces captured Obi - Wan Kenobi on Geonosis and charged him with spying for the Republic . Anakin Skywalker and Senator Padmé Amidala attempted to rescue Kenobi , but were also captured and sentenced to death . A Jedi strike team led by Mace Windu stormed the Petranaki arena , where the prisoners were to be killed . The ensuing battle resulted in the deaths of many Jedi and the bounty hunter and template of the clone army , Jango Fett . This was the first time the Jedi have ever faced B2 Super Battle Droids and were overwhelmed by their upgraded intelligence , armor , and weapons . The Jedi managed to hold their own for some time but were being beaten back by the outnumbering droid forces . As they prepared to fight to the end , the clone army , under Yoda ' s command , dropped from the sky in Republic gunships . Managing to rescue the Jedi from the arena , the clones engaged the droid army on the fields of Geonosis , in order to prevent their escape . However , the battle on the surface was not the only conflict . In the space battle , the clone pilots , led by Adi Gallia , took out valuable Trade Federation battleships , and in the subterranean battle , fought between clone commandos — most notably the commandos of Delta Squad — and Separatist forces , saw victory for the Republic by eliminating foundries and Geonosian leaders , such as Sun Fac . Count Dooku , after the battle lost , took the plans for the Separatists ' Ultimate Weapon and fled to a secret hangar . Intercepted by Kenobi and Skywalker , he managed to best them both , even severing Skywalker ' s right arm at the elbow . However , he was unable to defeat Yoda as easily , and was forced to resort to trickery in order to escape . Traveling to Coruscant , Dooku met with Darth Sidious at The Works . It seemed clear to the two Sith Lords that , while the Battle of Geonosis was a defeat , it was but the first move in a much larger game . Year one ( 22 – 21 BBY ) . Strategies . Although the Battle of Geonosis was a victory for the Republic , the prospect of a war between the Republic and the Confederacy was now inevitable . Millions of clone trooper units departed from Coruscant on missions to find and defeat the Confederacy . The clones were led in these missions by the Jedi Knights , the first time that the Jedi Order had taken up arms en masse since the Seventh Battle of Ruusan a thousand years prior . Despite the scale of the opening battle of Geonosis , however , neither side yet had the resources or the strategy to fight a major galactic war . The Republic in particular was bedeviled by the fact that at this early stage the Grand Army of the Republic numbered only 3 million troops ( it would eventually be expanded many times over ) . To coordinate the strategy of the war , Supreme Chancellor Palpatine ordered the establishment of the sector armies , large military commands that operated within theatres known as oversectors or priority sectors , areas of operations that overrode old sector boundaries . Each sector army initially numbered 150 , 000 clone troopers , numbers which expanded dramatically as the war went on . Under the command of the new Jedi Generals , the sector armies served as rapid reaction forces while the Republic ' s disparate Planetary Security Forces operated in defensive deployments - a number of battles in the Clone Wars were fought entirely by Planetary Security Forces without a clone trooper or a battle droid in sight . Each sector army was divided into four subordinate corps , of which three were further divided into smaller components . Under the " 1 / 4 / 16 / 64 Plan " , one corps was maintained as a mobile reserve force while the others were divided into progressively smaller units so that one army could fulfill one corps operation , four brigade - level operations , sixteen regiment - level operations or sixty - four battalion - level operations . In reality , sector army deployments were rarely so neat , and typically one corps in each army remained intact , but the others were divided into hundreds of small , fast - moving raiding companies . Known as the " militia model " , this allowed small numbers of clone troopers to mobilise far larger numbers of local guerrillas and execute planetary coups , a strategy that was successful at the Battle of Malastare , the Battle of Haruun Kal , and the Battle of Giju . Though it launched a few coordinated attacks in the first year of the war that were usually successful , for example , at Muunilinst and Dac , the Republic ' s war was typically a defensive one , with most offensive operations being small - scale raids . The few pockets of Separatist space in the Core , for example , Cato Neimoidia , Scipio , Castell , and Foerost , were blockaded . Until it could build up its armed forces to overwhelm the Confederacy , the Republic was vulnerable to the Confederacy ' s stateless strategy . The Separatists pursued a defensive strategy for the first few months of the war , seeking to blunt Republic drives into their dispersed territories . Its first offensive moves were combinations of surgical strikes and terror operations , a stateless strategy designed to deny the Republic key invasion corridors , undermine support for the war , and sever key fleets ' supply lines . Dooku rapidly moved to secure key hyperspace nodes to ease the future deployment of the Separatist Droid Army , as well as for occupying whatever opportunistic pockets of space declared themselves . The Confederacy quickly secured the hyperspace crossroads of Yag ' Dhul on the Rimma Trade Route and the Corellian Trade Spine , as well as Sluis Van , solidifying their hold on the southern Rimma . Other early gains included the Abrion sector , which provided the Confederacy with some 200 agricultural worlds , as well as a route to the Rishi Maze and Kamino . Another gain was the Lahara sector which brought over Agamar , Oorn Tchis and the Mirgoshir hyperspace crossroads , thus linking the Confederacy ' s territories from Muunilinst to the Outer Hydian . Other disaffected alien homeworlds that came over included Ando , Tynna , and Sy Myrth ( though Ando joined the Confederacy , the Andoan Free Colonies remained loyal to the Republic ) . Finally , a corridor of Mid Rim industrial worlds in the northern Slice including Metalorn , Saleucami and Quermia declared for the Separatists , forming the core of the CIS ' industry and becoming known as the " Foundry of the Confederacy " . To compensate for their disadvantage in resources , the Separatists also sought a technological advantage , manifested in a resort to superweapons and bioweapon s . Before they could build up their armed forces for a strike at the Republic ' s core , however , much like the Republic ' s strategy , the CIS ' war typically took the form of a large number of small - scale raids . Both sides also pursued a furious propaganda battle , the Republic through HoloNet News , and the Separatists through the CIS Shadowfeed . The Northern Campaign . The raiding strategy . Both sides made a handful of large offensives in the first year of the war : In the Republic ' s case , the Muunilinst campaign , the Ninth Army ' s push north towards Agamar in an effort to break the Separatists ' lines of communication from Muunilinst to the Outer Hydian , the Twelfth Army ' s early advance up the Perlemian from Lantillies to Centares , and the Eleventh Army ' s battle at Florrum to create a salient to separate the Separatist enclaves on the Outer Hydian and Perlemian . In the Separatists ' case , the Hunt for the Decimator and the Dark Reaper Crisis . However , the majority of operations consisted of small scale raiding . The Republic raided to Pengalan IV to destroy a diamond boron missile s facility in the city of Tur Lorkin . These missiles were outfitted with a shell too tough to be destroyed by a starfighter ' s laser cannons and when they exploded their massive blast radius could take out several small ships . The Republic had to destroy the factory or their fighter squadrons would be slaughtered . To the relief of every GAR fighter pilot they pulled it off . Later , Mace Windu was sent to the moon Ruul to investigate reports of defecting Jedi . Ruul was the private estate of Sora Bulq , who called a meeting of the Jedi dissidents refusing to fight in the so - called Clone Wars . Secretly , he hired the dark assassin Asajj Ventress to kill the Jedi , but Mace Windu was able to uncover Bulq ' s treachery and drove the assassin away . On Axion , a Colicoid engineer involved in the creation of Protodeka s was located on the planet , thus making Axion a prime target for the Republic . A clone trooper force under command of Commander Brolis was sent in to infiltrate the fortress , but the Colicoids managed to call for reinforcements . Soon , an army of droids arrived on Axion and eventually the Republic task force was reduced only to Brolis , who was trapped in a ruined apartment . His calls for reinforcements were ignored by the Republic High Command . It seemed that Brolis was doomed until he met Jedi Master Yoda — his only reinforcement . Yoda then engaged an attack wave of battle droids with his lightsaber and then in a brilliant display of " size matters not " , he destroyed a Hailfire droid by using the Force to trick it into burying itself under twelve tons of collapsing rock . Though Yoda and Brolis escaped , Axion was lost to the Confederacy . In the aftermath of the Battle of Christophsis , Jedi Master Aayla Secura and Clone Commander Bly captured an important Separatist T - series tactical droid on a planet . Secura and Bly were later ambushed over the planet Quell . The Battle of Quell began shortly afterwards , as Secura ' s ships were assaulted by rocket droids , Jedi Skywalker and his apprentice Ahsoka Tano , arrived and helped Bly and Aayla evacuate the decimated Republic Cruiser . Before the Jedi could dock aboard the " Resolute " to give a wounded Skywalker medical attention , fire from droid fighters knocked out one of the pilots , accidentally activating the hyperdrive . Admiral Wullf Yularen managed to maneuver the " Resolute " out of the way , preventing the ship from being taken into hyperspace with the frigate . After a treacherous trip through hyperspace , the Jedi and the few clones in their company crash landed on the planet Maridun . Secura and Tano soon found a village of Lurmen who had settled on the planet , far away from the war . The village elder , Tee Watt Kaa refused to aid them , fearing that destruction would break the peace they already had . However , at Tano ' s request , he did give them medical supplies and had his son , Wag Too to help deliver them . But he requested that only one Jedi was to take the supplies and that CC - 5052 should follow . A Separatist force arrived , and the Jedi and clones retreated in order to protect the village . When they discovered that the Separatist forces were there to test a new weapon that only destroyed organic matter , they rushed to save the village . In the battle that insured the Jedi defeated the battle droids that attacked , though Skywalker proved to be the one who destroyed the prototype weapon . On Lianna , Jedi General Cei Vookto and clone troopers under his command would defend a Sienar Fleet Systems starfighter facility from invading Separatist forces . With Raith Sienar ' s designers working on new starfighters for the Republic Navy , it was not a planet the Republic could afford to lose . The battle raged across Lianna , with losses on both sides . Leading the campaign , Master Vookto used his powers of elemental summoning to cleanse the planet with twin pillars of water and fire . The toll this took on Cei Vookto cost him his life . Upon Vookto ' s death , Ki - Adi - Mundi assumed command of his surviving forces . Following his revelation to the Jedi Order at the Battle of Hypori , General Grievous had his battle droid forces on Ord Mantell raze an entire civilian township to divert Republic troops and allow himself to escape . Subsequent Separatist raids led to the capture of critical hyperlanes running to Dac and Kessel , jeopardizing the Mon Calamari and supplies of spice to the Republic , totaling six Separatist victories that month . Meanwhile , Eeth Koth led his troops to defend the besieged people of Korriban . As part of the Eleventh Army ' s drive to separate the Confederate enclaves on the Perlemian and the Hydian , the Commerce Guild ' s planet Felucia was targeted . High Jedi General Obi - Wan Kenobi , Jedi General Anakin Skywalker , and Jedi Commander Ahsoka Tano were dispatched with a clone trooper detachment of the Grand Army of the Republic to take the planet . The Jedi and their forces soon began to be overwhelmed by the Separatist battle droids , however , and Republic reinforcements were sent to extract the troops from the planet . While Republic Star Destroyers engaged the Separatist blockade surrounding Felucia , Jedi Master Plo Koon led several LAAT / i gunships and their starfighter escorts to rescue the Jedi and clone troopers on the surface . After Skywalker , Kenobi , and their troops abandoned their AT - TE walkers to escape on the gunships , Kenobi contacted Tano , who had led a squad on a jungle patrol and had separately engaged the droid army . Though Tano initially refused to retreat , the gunships landed between her forces and the droids , forcing the Padawan and her squad to abandon their fight and escape . Just as the gunships retreated , the AT - TE walkers and the Juggernaut tank that Tano had left behind were blasted apart by a large group of battle droid reinforcements . The Republic retreated , leaving the Confederacy victorious on Felucia . The Muunilinst campaign . One of the largest campaigns of the first year of the war was the Republic Eighth Army ' s drive to capture Muunilinst . When word reached the Jedi High Council of the InterGalactic Banking Clan ' s construction of droid armies on the planet , Chancellor Palpatine dispatched Anakin Skywalker and Obi - Wan Kenobi to lead an assault on the planet , with Kenobi commanding the clone forces on the ground and Skywalker , at Palpatine ' s suggestion , commanding the Navy forces in space . The planet was acting as the base world for the Banking Clan , and their chairman , San Hill , was a known member of the Separatist Council , so it was a prime target for the Republic . During the battle , the Republic unleashed a fleet of " Acclamator " - class assault ships on the Separatist defenses . The Republic forces soon clashed with the enemy forces , both on the ground and in space . On Muunilinst , Kenobi ' s army quickly took the advantage . An elite group of Advanced Recon Commandos under command of Captain Alpha - 77 , known as " The Muunilinst 10 " , were on a mission in the city of Harnaidan , though their gunship was shot down behind enemy lines . The ARC Troopers , however , completed their mission , to destroy a massive defensive artillery emplacement at the heart of Muunilinst . SPHA - T artillery decimated huge sections of the city and Separatist forces . In reply to this , the Separatist bounty hunter Durge led an squadron of IG lancer combat droid s against Kenobi ' s ground forces . The strike force cut swaths through the columns of SPHA - Ts and their trooper protection . In response , Kenobi led a force of clone lancer trooper s on 105 - K lancer bike s and defeated Durge ' s force , with Kenobi even defeating Durge in single combat . He then met up with the Muunilinst 10 at the InterGalactic Banking Clan ' s Command Center , and after a brief skirmish , took San Hill and his associates into custody . It was then that , Durge , who had survived the first duel , appeared and charged into the command center , where he was met with a volley of fire from the troopers . He was badly damaged , but survived thanks to his unique Gen ' Dai abilities and attacked Kenobi . Many clones were killed , but Durge was eventually defeated by Kenobi with aide from Captain Alpha - 77 . The surrender of the Banking Clan leadership spelled victory for the Republic . However , due to his regenerative abilities , Durge was able to survive . Meanwhile in space , Anakin Skywalker was leading the Republic forces to victory . During the space battle he used an unorthodox move : ordering the clone fighters to shoot their missiles in a direction that looked clear of enemy units , across the bow of an " Acclamator " - class assault ship . As Anakin flew up past the Republic battleship , many droid starfighters followed him . The missiles just missed Anakin , but destroyed numerous fighters . He then flew past a Separatist cruiser , while the remaining missiles , still tracking his position , were led into the hangar . The ship was destroyed . Later in the battle , a mysterious starfighter dropped out of hyperspace , destroying many clone - piloted starfighters . Skywalker immediately engaged the unknown ship in a space duel . The heated , twisting dogfight raged from orbit , down to the surface and then back into space again . When the pilot , a mysterious Force - sensitive protégé of Dooku later revealed to be the infamous Asajj Ventress , jumped into hyperspace , the impetuous young Jedi followed , disobeying a direct order from Kenobi . He pursued her to the jungle moon of Yavin 4 . Though she initially managed to stay hidden from Anakin , she made her presence known when she stealthily killed an entire squadron of clones that Kenobi sent after Anakin and blew up his starfighter . They soon engaged in a lightsaber duel through the jungles and finally led to the top of a Massassi Temple . In the end , Ventress was defeated , though not killed . Despite this , the Republic had won another major victory against the Confederacy . At the same time , the Confederacy was using the planet Dantooine as a staging point to launch a counterattack against the Republic blockade around Muunilinst . However , Jedi Master Mace Windu learned of the Confederate presence on Dantooine and left with a force of clone troopers to halt the progress of the Separatists . War erupted on Dantooine as clones and droids clashed in a vast , open plain . With Master Windu at their side , the clones quickly gained the upper hand , despite being outnumbered nearly four to one by Confederate B2 super battle droids . However , the battle was suddenly turned upside down with the arrival of a large siege weapon — the seismic tank . This tank used its seismic driver — once used in peace - time for mining operations — to cut a swath through the clone trooper ranks , either crushing them outright or sending soldiers flying from the shockwave . In the confusion , Windu lost his lightsaber , and was forced to fight a number of droids unarmed . Retrieving his lightsaber amid another seismic shockwave , Windu flew toward the seismic tank . Windu cut his way in , disabled the seismic driver , destroyed the tank ' s droid crew , and knocked out the controls . Flying clear , Windu watched on as the seismic tank smashed into the ground and exploded . The battle was won for the Republic . The Battle of Mon Calamari . Meanwhile , on the ocean planet Dac , the Mon Calamari Knights under the Jedi Master Kit Fisto defeated the Separatist - backed Quarren Isolation League . After the battle , Kit Fisto discovered the League was allied with the Moappa , whom Kit discovered were also sentient . Kit informed the Mon Calamari that they needed to make peace with and respect the sapience of the Moappa . Despite the defeat , many members of the predominantly Quarren Free Dac movement fled Mon Calamari , settling on the Separatist worlds of Pammant and Minntooine , where the Free Dac Volunteers Engineering Corps created shipyards . Using designs based on Mon Calamari Shipyards blueprints stolen by the Separatists as a basis , these yards created " Recusant " - class light destroyers at Minntooine and " Providence " - class carrier / destroyers at the Pammant Docks for the Confederate Navy . The Southern Campaign . The defense of Kamino . With a route to the Rishi Maze secured via the Abrion sector , the Separatists launched an assault on Kamino . Separatist forces under the Corporate Alliance Magister Passel Argente and the Mon Calamari Merai assaulted the ocean planet in an attempt to destroy the Republic ' s cloning facilities . However , the Jedi learned of their plans and sent a defense fleet of Jedi starfighters to defend Kamino . Although the Jedi pilots battled bravely above , they could not stop the droid forces from landing in Tipoca City . The arrival of the newly - activated ARC troopers and Jet Commandos served to turn the tide , and Merai was forced to launch a desperate strike at the supposed location of the city ' s shield generator . However , the Jedi proved too wily for the Mon Calamari tactician ; the data gathered by the Corporate Alliance was false , and Merai ' s efforts were in vain . In a last - ditch attack , Merai flew into the Jedi hyperspace rings , destroying his personal starfighter the " Shark " in the process , giving his battleships time to retreat . Though apparently a victory for the Republic , the battle was actually engineered by Darth Sidious and his apprentice Darth Tyranus to root out and destroy the traitors in the Confederacy . Following that , more clone troopers from Kamino were deployed , thus allowing the war to continue . The Republic also began research into other methods of cloning such as Spaarti cloning cylinder s and conscription was introduced throughout the Republic . Christophsis , Teth , and the Hutts . Within four weeks of the Battle of Geonosis , the Confederacy swiftly seized many major hyperspace lanes , denying the Republic access to them and preventing the Jedi from gaining a foothold in the Outer Rim . The Separatists soon set its sights on the Outer Rim ' s resource - rich planet Christophsis . Admiral Trench , who had been presumed dead at the Battle of Malastare Narrows , blockaded Christophsis with a large fleet , trapping Senator Bail Organa on the surface with his refugee camp , as well as separating the Republic from several of its key armies . Skywalker , who had by this time been made a Jedi Knight , set out with Admiral Wullf Yularen to break Trench ' s blockade and rescue the trapped Organa . After Skywalker ' s initial assault on the Separatist blockade was repelled , Kenobi arrived with an experimental stealth ship that was equipped with a cloaking device , which Skywalker used to great effect in destroying Trench ' s flagship , the " Invincible " , and delivering relief supplies to Organa ' s camp on the surface . After breaking through the remnants of Trench ' s blockade , Kenobi landed on Christophsis with the main body of troops , and their forces prepared an assault on the Separatists . Although a clone traitor — Sergeant Slick , who had betrayed his comrades to Asajj Ventress — hindered the Jedi in attempting to ambush the Separatists in Crystal City , Commander Cody and Captain Rex discovered the spy ' s allegiances and apprehended him . Skywalker and Kenobi also dueled Ventress while searching for information behind enemy lines and discovered that the Separatists were landing hundreds of droid troops to secure Christophsis . Skywalker , Kenobi , and the new addition of Padawan Ahsoka Tano , who had been assigned to Skywalker , battled the Confederate General Whorm Loathsom ' s thousand - strong droid army on Christophsis and were eventually able to capture Loathsom and free the beleaguered world from the Separatist occupation , with help from reinforcements under the command of Yularen and Master Yoda . While all of this was going on , however , Count Dooku set his own plan into motion to sway the Hutt families to the Confederate side . He first had Ventress capture Rotta , the son of crime lord Jabba Desilijic Tiure , and when Skywalker and Tano went to rescue Rotta at the B ' omarr Order monastery on the jungle planet Teth where he was being held , Dooku deceived Jabba into believing that the Jedi and the Republic had in fact kidnapped his son . Furthermore , Ventress was sent to Teth to kill the Huttlet and blame the Jedi for the crime so that Jabba would take revenge on the Jedi , at which point Jabba ' s uncle , crime lord Ziro Desilijic Tiure — who had secretly assisted Dooku in capturing Rotta — would be able to take Jabba ' s place at the head of the Hutt families , as Jabba would be arrested by the Republic for avenging his son ' s death . However , while Rex and the 501st Legion ' s Torrent Company battled Ventress ' s army , Skywalker and Tano were able to prevent Ventress from retrieving Rotta . As Skywalker and Tano traveled to Tatooine to return Rotta to his father , Kenobi arrived to reinforce Rex ' s men on Teth and dueled Ventress in the monastery , ultimately forcing Ventress to retreat from Teth and defeating her droid army . Skywalker and Tano , meanwhile , were shot down over Tatooine by Dooku ' s forces , but after battling Dooku himself and a squad of MagnaGuards , respectively , Skywalker and Tano were able to reach Jabba ' s Palace and exposed the Separatists ' plot . While Dooku escaped Jabba ' s wrath , the crime lord signed a treaty with the Republic that granted the Grand Army much - needed access to Hutt Space ' s hyperlanes , and the Hutts became allied to the Republic . In addition , Senator Padmé Amidala spearheaded the arrest of Ziro at his palace on Coruscant . The Battle of Ryloth . Techno Union Foreman Wat Tambor set out to conquer the planet Ryloth for the riches that rival Separatist Magistrate Passel Argente had secretly stowed there . The Twi ' leks on the world were subjected to a brutal droid occupation and were starved . While Jedi General Ima - Gun Di and Twi ' lek resistance leader Cham Syndulla defended the planet from the Separatists , Senator Bail Organa and Representative Jar Jar Binks were able to gain permission from King Katuunko of the neutral Toydaria to use his world as a staging ground for supply ships that would deliver rations to the starving Twi ' leks . Though Di and his forces were ultimately defeated , Syndulla ' s resistance survived and used the Republic ' s delivered food and medical supplies to great effect . Having seen the good that the Republic did for the Twi ' lek civilians , King Katuunko agreed to meet with Master Yoda on Rugosa to discuss bringing Toydaria into the Republic . However , Count Dooku caught wind of the planned meeting and sent Ventress to convince Katuunko that the Separatists represented more of the Toydarians ' interests . After being shot down by a Confederate fleet on Rugosa , Yoda and his team of three clone troopers — Commander Thire , Jek , and Rys — bested Ventress ' s battle droid army in a contest of strength , winning Katuunko over to the Republic side . Ventress tried and failed to assassinate Katuunko for his new loyalties , and while she fled from Rugosa , Yoda and Katuunko began the process of discussing a treaty for Toydaria ' s new allegiances . Following its successful defense of Kamino , the Republic ' s Fourteenth Army launched an attack of its own to free occupied Ryloth . Skywalker , Tano , and Yularen were sent with a Republic fleet to breach Separatist Captain Mar Tuuk ' s blockade of Ryloth so that Kenobi and Mace Windu could land with the main assault force . Although Tano ' s Blue Squadron was unable to break the blockade in their initial assault and was forced to retreat with the rest of the fleet , Skywalker used the damaged cruiser " Defender " to return to the Ryloth system and rammed it into Tuuk ' s flagship , forcing Tuuk to flee from the battlefield . Tano and Yularen then entered the system with Skywalker ' s flagship , the " Resolute " , and cut through the droid defenses , allowing Kenobi and Windu to safely approach the planet . However , the Republic invasion fleet was prevented from landing on Ryloth by a group of heavy proton cannons that had been stationed in the city of Nabat with T - series tactical droid commander TX - 20 . Once Kenobi , Commander Cody , and Ghost Company had infiltrated Nabat , taken out the cannons , and defeated TX - 20 and his droid forces , Windu landed with the main body of troops and headed to retake the captured capital of Lessu . While Skywalker finished securing the space around Ryloth and Kenobi took the Jixuan desert , freeing most of the planet ' s southern hemisphere , Windu headed for Lessu with Commander Ponds and Lightning Squadron . After suffering losses in a battle with the droids on the way to Lessu , Windu enlisted the help of Cham Syndulla , who despite holding a grudge against Ryloth ' s senator , Orn Free Taa , agreed to ally his forces with the Republic if it meant a free Ryloth , in exchange for a promise from Taa that Ryloth would not be occupied by the Clone Army after it was freed . Combining forces , Windu ' s Lightning Squadron and Syndulla ' s freedom fighters were able to retake the occupied Lessu and took Tambor into custody , and a parade was held in Lessu following their victory . However , the threat to Ryloth was not over , as many of the pockets of Separatist resistance continued to hold out against the clone forces . Skywalker and Tano were charged with mopping up the droid resistance on Ryloth , and did so to great effect . A new threat soon took the form of the Separatist scientist Kul Teska , who — after attacking Windu , Kenobi , and Plo Koon on the space station Juma 9 — traveled to Ryloth in pursuit of the bounty hunter Cad Bane , who had stolen a part of his gravitic polarization beam weapon . While Skywalker and Tano fought with Teska , Jedi Generals Aayla Secura and Luminara Unduli dueled Asajj Ventress on the ice world Alzoc III , where Bane had sabotaged a part of the gravitic polarization beam . Although both Teska and Ventress escaped from their respective combatants , Skywalker , Tano , Kenobi , and Windu were able to destroy the gravity weapon at its construction facility on Behpour and also killed Teska . Raids in the south . One of the first truly costly battles fought by the Republic was the defense of Teyr from a Separatist raid . The 416th Star Corps , under command of the Whiphid Jedi Master K ' Kruhk , were sent to destroy a downed " Lucrehulk " - class battleship that the Trade Federation was using as a base . K ' Kruhk led his forces through the Great Canyon , only to have many of his men shredded to pieces by spider droids . K ' Kruhk ' s battalion made it to the lip of the canyon , and made a final assault . K ' Kruhk led his troops from the front , but knew the Separatists had the advantage in numbers . He ordered his clones to fall back , but they assured him they could achieve victory . K ' Kruhk was unprepared to send so many men to their deaths , though the clones knew this is what they had been bred for ; to fight and die in battle . With a weary heart , K ' Kruhk pressed the attack , and though the battleship was destroyed , only the Jedi General , CRC - 09 / 571 , and several clone troopers appeared to have survived the battle . On Coruscant , a group of Korun nai terrorists took Senator Meena Tills hostage as part of an attempt to turn the Corporate Sector against the Republic . However , their efforts were thwarted by Omega Squad . Around this time , the Separatists also finished creation of the Storm Fleet , a secret fleet of powerful destroyers that was meant to conquer planets with their large amounts of firepower , and dispatched it to Cyphar . Anakin Skywalker and Obi - Wan Kenobi managed to stall the fleet at the Llon Nebulae so the Republic could send a fleet to defend the planet . They succeeded ; more than half of the Storm Fleet was destroyed , and Cyphar remained in Republic hands . The Battle of Praesitlyn was a Confederate attempt to solidify its presence on the southern Rimma Trade Route by conquering Praesitlyn . Despite possessing an advanced communications center that linked data feeds throughout the galactic quadrant , the planet had few defenses . The Republic fleet was lured away from the planet by a blockade of Sluis Van , and a fleet under the Banking Clan Admiral Pors Tonith conquered Praesitlyn with a massive invasion army . Their efforts were sped up thanks to a system - wide jamming field unleashed by Tonith ' s fleet . This prevented communication with the rest of the galaxy . Captain Zozridor Slayke of Freedom ' s Sons attempted to stop the Separatists , though his forces were nearly defeated . Luckily , Republic reinforcements under Nejaa Halcyon and Anakin Skywalker arrived just in time . This resulted in the Battle of Praesitlyn . During the battle , the Republic and the Sons and Daughters of Freedom were pitted against over one million battle droids and a large space fleet . The battle had the distinction of being the final trial for Skywalker before becoming a Jedi Knight . On Hypori , one of the greatest threats the Republic would face during the war made his dramatic debut . Jedi Master Daakman Barrek led a force to destroy a droid factory thought to be on the planet . However , the attack was a disaster , with orbital mines shredding much of the force as it emerged from hyperspace , and General Grievous led a massive droid army in the the obliteration of an entire Republic army and the deaths of several Jedi , including Tarr Seirr , Daakman Barrek and Sha ' a Gi . Only the timely intervention of ARC Captain Alpha - 77 and a squad of ARC Troopers sent from General Kenobi on Muunilinst prevented the remaining Jedi from being killed as well . Only Shaak Ti , Ki - Adi - Mundi , Aayla Secura , K ' Kruhk and the ARC squad , survived the battle . The Republic and CIS fought the Battle of Orto Plutonia after Kenobi and Skywalker were called to Orto Plutonia to ascertain why the Republic had lost contact with a clone outpost there . The Jedi and clones were accompanied by Chairman Chi Cho of Pantora and Senator Riyo Chuchi , who had been recalled to the Pantoran system by Cho so that he could use her Senatorial authority to command the Jedi . Orto Plutonia was technically under the control of the Pantoran Assembly , and as such , Cho felt that he should be directly involved in the Jedis ' investigation . With clone Captain CT - 7567 , General Kenobi found the Republic base to be devoid of life , all clones stationed there having been killed . Similarly , they found a nearby Separatist base to be likewise affected and found clues of a third party being involved in the demise of both forces . Skywalker and Kenobi then followed clues to a nearby canyon , where they spotted light reflections . Shortly afterward they met primitive , but sentient , inhabitants ; the Talz . Despite the language barrier , Kenobi and Skywalker managed to make it clear that their mission was one of peace , and they arranged a diplomatic meeting between the Pantorans and the Talz . When they delivered the news , Chairman Chi Cho arrogantly refused to believe that the Talz could be considered a sentient race and called them trespassers and animals , stating that Pantora hadn ' t evidence of life on the planet in all their history . Riyo Chuchi tried to mediate , feeling that it was for the Senate to decide the matter , but to no avail . Upon arrival at the meeting place , the Talz leader , Thi - Sen , politely asked that the Republic leave them in peace and withdraw their presence from Orto Plutonia . However , Chi Cho still refused to accept the Talz as sentients and arrogantly declared Plutonia as sovereign Pantoran property , deliberately provoking a war . In order to gain sanctity for his actions , he declared this to be an internal affair of Pantora ; so as to remove the Jedi from the equation . Skywalker and Kenobi appealed to Riyo Chuchi , to find a way to resolve the political matter diplomatically . In response she contacted the Speaker of the Pantoran Assembly , who granted her the authority to negotiate peace and declared the Chairman out of order . However , this solution came too late : while returning to their base , Chi Cho and his escort were ambushed by a Talz war party , forcing them to fight back , and Chairman Cho was felled by a spear in his back . Skywalker , Kenobi and Senator Chuchi arrived in time to save Cho , CT - 7567 and the remaining escort from being overrun , but even with his last breath , Cho insisted on killing the Talz for the ' good ' of his people as his final command . Chuchi politely declined , informing him of the Assembly ' s decision . Dumbfounded that he was overruled and that his people preferred peace to war , Cho expired . Senator Chuchi pursued a peaceful approach and managed to cease hostilities , conceding sovereignty of Plutonia to the Talz . As she and the Jedi boarded a gunship off - world , Kenobi stated that to maintain peace , she should make it last . The Battle of Malastare began when the Droid Army attempted to seize the planet and its vital Dug fuel resources . Joining forces with the Dug Council , the Republic attempted to stop it with the use of a new superweapon the electro - proton bomb by orders of Chancellor Palpatine . Although it succeeded in depleting all the droid numbers , the bomb awoke a Zillo Beast and it unleashed its reign of terror on Malastare . Eventually the beast was knocked out by the Republic ' s stun tanks and it was taken back to Coruscant for study to unlock the secret of its impenetrable scales . With the Dugs convinced that the beast was dead , they signed the treaty and Republic was able to use Malastare ' s fuel reserves to power its expanded star fleet . Palpatine hoped that if the Beast was studied , scientists would uncover the secret of its highly impenetrable scales , resistant to explosives , blasterfire and lightsaber strikes , creating thus a new generation of clone trooper armor . During its stay on the Galactic Capital , the Beast escaped and wreaked havoc until it was Killed using the Malastare fuel toxican . Soon after Chancellor Palpatine secretly ordered Dr . Sionver Boll to clone the extinct beast . In the aftermath of the " Malevolence " chase , General Grievous once again set his sights on Kamino , home to the Republic ' s vital cloning facilities . In collaboration with Ventress as his agent on Kamino , Grievous advanced his invasion fleet through the Rishi system and sent a squad of BX - series droid commandos to secure the Republic base there and hot - wire its " all - clear " signal so that the Republic would not learn of his attack . Although the droid commandos were able to do so , several clones — Hevy , Fives , Cutup , and Echo — were able to escape from the droid assault . Though Cutup fell prey to a Rishi eel , Hevy , Fives , and Echo came under the command of Captain Rex and Commander Cody , who had stopped at Rishi Station during an inspection run of several of the Republic ' s listening posts and tracking stations . The clones were able to retake the base , and though droid reinforcements sent by Grievous threatened to recapture the station , Hevy sacrificed himself to destroy the station , cutting off the base ' s " all - clear " signal and warning the Jedi of the impending assault . Skywalker , Kenobi , and Yularen promptly arrived and drove Grievous ' s forces out of the system , thwarting his attempt to invade Kamino . In the lead - up to the Battle of Bothawui , General Grievous led Separatists forces to fight on the planet Anoth and battle on the planet Bakura , engaging Skywalker and Kenobi both times . Concurrent to his victories in the north that endangered Dac and Kessel , Grievous also captured crucial hyperlane s running to Bespin . The capture of the lanes jeopardized supplies of tibanna gas , leading to civilian suffering . While Grievous set his sights on the planet Bothawui , home to the crucial Bothan Spynet that was a key affiliate of Republic Intelligence , members of the Jedi High Council personally and actively led several campaigns . Ki - Adi - Mundi undertook a mission to Barab I , and Adi Gallia led clone forces in the Battle of Agomar . Meanwhile , Count Dooku had his forces liberate the planet Lanos from the occupying Republic forces in a battle that was subjected to a high amount of anti - Republic Separatist propaganda , much to the Jedi Council ' s chagrin . When Kenobi learned of Grievous ' s impending attack on Bothawui from his friend Dexter Jettster , the Jedi Council decided to take action , sending Skywalker , Tano , and Yularen with a fleet to protect Bothawui . Grievous overwhelmed a Republic task force on Falleen on his way to Bothawui but then fell into a trap that Skywalker had set for him . In the ensuring Battle of Bothawui , Grievous ' s forces were defeated , but the astromech droid R2 - D2 — whom Skywalker had never subjected to a memory wipe and who thus had a multitude of Republic war operation intelligence — went missing in the battle . R2 - D2 was found by the scavenger Gha Nachkt and promised to Grievous . After conducting an unsuccessful search for R2 - D2 , Skywalker returned his cruisers to the Allanteen Six shipyards where they had been manufactured to carry out some modifications . R2 - D2 was successfully recovered from Skytop Station over Ruusan 2 by Skywalker , Kenobi , and Tano . The Battle of Haruun Kal began six months after the battle of Geonosis with the dispatching of Senior Jedi Councilman Mace Windu to his home planet of Haruun Kal . A holovid recovered by the Republic had shown Master Depa Billaba , who had been dispatched by the Council to train the Korun nai natives against the Separatist - backed Balawai settlers , in a state of what appeared to be bloodthirsty insanity . Billaba had been sent to the planet because although its location was of strategic importance for trade , the Republic was not yet ready to commit to a full offensive against the world . After surviving an assassination attempt orchestrated by a treasonous Republic agent and journeying upcountry to confront Billaba , Mace led the Korunnai troops , in concert with clone reinforcements under the command of CRC - 09 / 571 from the Republic transport " Halleck " , against the Balawai militia . He moved against the capital city of Pelek Baw and using an ingenious strategy that combined sneaking in transports down the path of a waterfall , eventually managed to corner Balawai militia Colonel Lorz Geptun . Despite a last - minute betrayal by a number of elite Korunnai soldiers led by the dark Korunnai Kar Vastor , Windu forced Geptun to surrender the system and shut down attacking droids . This victory came at a heavy cost , however , as Billaba fell into a possibly self - induced coma at the end of the battle from which it was believed she never recovered . Separatist superweapons . The Hunt for the Decimator . The Hunt for the Decimator was the first large campaign of the war . Seeing the advent of war , the Wookiees started the Decimator for the Grand Army of the Republic in the Erediss system and Alaris Prime . Its existence was learned by Bogeega Bu ' Daay , an operative who informed the Hutt Cartel and Boorka the Hutt ; Boorka understood that the information would be fruitful if he gave it to the Separatists . Dooku ordered his most trusted General , a Dark Acolyte named Sev ' rance Tann , to capture the Decimator for the Confederacy . Tann was sent to the Kaer Orbital Platform in the Siskeen system with a small force and established a base . Fighting her way through mynocks she employed DSD1 dwarf spider droids and OG - 9 homing spider droids and defeated the Republic task force under the command of Jedi General Jor Drakas who Contacted for reinforcements from a closer Fleet . Soon , before the Republic captured and reclaim the orbital platform , Tann ' s new droid army was finished and Dooku sent transports to ship the new forces to Tatooine & Raxus Prime to reserve them for the conquest of Sarapin and its defense . Meanwhile , Sev ' rance along with the B2 super battle droids and some Droidekas set course to Tatooine in a mission to find the most powerful weapon of the Republic . She learned that Boorka , a Hutt , had valuable information for the Separatists . After impressing Boorka , the Hutt agreed to give her his information concerning the Decimator on Eredenn Prime when Tann destroyed the Republic spaceport nearby . At Dooku ' s command , Tann ' s army quickly exterminated the garrison of Eredenn Prime commanded by Kraen Weest . She attacked both Shard Test Site and Facet Test Site , capturing their Decimators and several Decimator Facilities intact . However , she lacked the control codes to make them operational , located in a nearby control center . The Wookiee ' s support of the planet ' s army arrived too late but helped some clones escape the massacre with the Activation codes to Alaris Prime . Tann seized a data droid possessing the codes from the Decimator Laboratory but not the fail - safe mechanism in order to use them . From the Laboratory , Tann also obtained the location of the Decimator manufacturing center on Alaris Prime and headed there next to decipher the codes necessary to use her new weapons . Tann then attacked Alaris Prime in order to get the codes from the Wookiees . Republic presence followed by the outpost Chendrrl , then Rwookawarrump , Llamitcuk , Tayriiwook , and finally Rwaawrrkoo attempted to stop Tann who established an island base . Sensing the need to disrupt reinforcements , Tann destroyed their transmitter tower and pressed on . In the end , she defeated the Republic and Wookiee forces , and secured the codes using a data droid . Tann then unleashed the collective droid forces she had been hiding on Raxus Prime and led them on Sarapin along with the stolen Decimator ; with it she destroyed the five key armies of the Republic that were stationed on the planet . She also killed Jedi General Jor Drakas and captured the Republic ' s citadel at Mount Corvast . The Decimators also destroyed the geothermal generators with blackouts on numerous Core Worlds as a result . The Separatists then established a new Decimator facility on Krant to continue production for the Separatists . A mining operation on the moon of Aereen was used for resources under Trade Federation purview Following the death of his apprentice , Stam Reath , on Geonosis , Jedi Knight Echuu Shen - Jon was assigned to retake Sarapin now under Separatist commander Zian Finnis . Echuu was accompanied by Naat Reath , Stam ' s sister ; together after finding the remains of a Decimator device , they fought off the Separatist forces and recaptured the citadel at Corvast . Finnis told the Jedi that the Hutt Cartel had knowledge of the whereabouts of Tann and once on Tatooine . Echuu and Naat met Jabba the Hutt who knew that Boorka was in league with the Confederacy and felt that his rival had gone too far . After helping the citizens of Mos Osnoe against Tusken Raiders , the two Jedi used their resources to build up a makeshift base from which they organized an assault against Boorka and then ( with Jabba ' s help ) against all Separatist presence on the planet . As a result they discovered a Trade Federation outpost on Aereen producing an army . Fighting their way through the security / sentry forces , the Republic forces made it to the main base and destroyed it , along with the Neimoidian leader Plure Barron . After the base ' s destruction , Echuu and his men went to Krant and joined by a number of Wookiee escapees from the Confederacy . Destroying several factories producing Decimators ( and even encountered a fully operational one ) and droid armies , Naat was kidnapped by Tann . Echuu found Naat and Tann with whom he dueled . Echuu let his emotions control him , and eventually defeated her through the aid of the dark side of the Force . Having destroyed the Decimator threat , and sending Naat back to Coruscant , Echuu began a self - imposed exile on Krant , an exile that would continue through the Great Jedi Purge . The Dark Reaper Crisis . In pursuit of another superweapon , Separatist forces commenced a massive attack on the seemingly unimportant Republic outpost of Rhen Var . Anakin and Obi - Wan managed to successfully evacuate most Republic presence there , but the Separatists took the planet regardless . Shortly afterward , the Republic sent Obi - Wan Kenobi and Anakin Skywalker to Raxus Prime where they discovered Separatist forces on the planet . Millennia earlier , in 3996 BBY during the Great Sith War , the Dark Reaper was unleashed upon the Jedi . However , the superweapon was disabled by Ulic Qel - Droma and would remain on the planet for millennia until Count Dooku and his Chistori mercenary Cydon Prax discovered an important component of the Reaper called the Force Harvester and unleashed a wave of energy killed roughly half of the thriving forest on Kashyyyk ' s moon , along with its indigenous population . The Sith Lord then took off and found the pieces of the Dark Reaper . The exact locations are not mentioned , but Mace Windu mentioned that it was separated into the farthest reaches of the galaxy . Dooku went to Thule and activated it in an ancient Sith city on the planet . Meanwhile on Rhen Var , Skywalker went to the grave of Ulic Qel - Droma for information on how to withstand the effects of the Dark Reaper . Shortly after the revival of the Dark Reaper , Skywalker led an attack on the city , destroying the weapon , disobeying an order from Obi - Wan Kenobi to await Republic backup forces . Despite Anakin ' s almost single - handed defeat of the Reaper weapon , his feats in these battles served to fuel his ego and create an even greater personal rift between himself and his master . However , the Confederacy managed to conquer Bespin and Ossus with the Republic preoccupied at the Battle of Thule . The Bio - Droid Threat . Meanwhile , the Jedi discovered a new type of Force - sensitive droid on Ord Cestus — the JK - thirteens . In response , Kit Fisto and Obi - Wan Kenobi were dispatched to the planet to ensure good relations with the Republic , to make sure these " Jedi - killer " droids were not being sold to the Separatists . Diplomacy failed , but the ruling Five Families were killed in a bombardment targeted by A - 98 . The mission and bombardment later proved to be hugely embarrassing for the Republic , as it was later revealed that the droids could neither be modified for lethality nor produced in great numbers , and that the Confederacy , in fact , had no real plans to do so . Chasing the " Malevolence " . A new Separatist threat soon took the form of the " Malevolence " , a massive ion cannon – equipped warship that had been manufactured at Pammant Docks . As it began its destructive run under the command of General Grievous , it executed a number of surprise attacks on Republic fleets , including an ambush in the Phu system , and left neither a pattern in its attacks nor any survivors to tell the Republic of the threat . With this growing threat , General Plo Koon set out with a fleet of cruisers to track down the weapon and found it in the Abregado system , where his task force fell prey to the " Malevolence " ion cannons at the hands of Grievous and Count Dooku , who was visiting the warship . Although the " Malevolence " killed most of the survivors of its initial attack , Skywalker and Tano — who had been stationed in the Bith system during the " Malevolence " assault on Koon ' s forces and were operating against the orders of the Jedi High Council — arrived in the system and rescued Koon and his fellow survivors of the clone squad Wolfpack , exposing the " Malevolence " true nature and costing Grievous the secrecy of his weapon . Despite losing favor in Dooku ' s eyes , Grievous continued to wreak havoc with the " Malevolence " , and after destroying a Republic fleet near Ryndellia , he targeted the Republic ' s secret Kaliida Shoals Medical Center — a station that was treating 60 , 000 wounded clone troopers — at Dooku ' s behest . After learning of the defeat at Ryndellia , Skywalker deduced that Grievous was targeting the Kaliida Shoals medcenter and immediately set out with Koon , Tano , and the Republic Navy ' s Shadow Squadron — aboard experimental BTL - B Y - wing starfighter s that he had acquired from a testing facility at Bormus without the Senate ' s approval — to intercept Grievous at the medcenter before he could destroy the station . Taking the Balmorra Run shortcut through the Kaliida Nebula , Skywalker and his squadron beat Grievous to the station , and though they were forced to abandon their original target of the " Malevolence " bridge due to losses inflicted by the warship ' s ion cannons and droid starfighter defenses , the Republic battle group compromised the warship ' s starboard ion cannon . When Grievous tried to fire the sabotaged cannon at the medcenter , which was still undergoing evacuation under administrator Nala Se ' s supervision , the cannon exploded , doing damage to the " Malevolence " and its hyperdrive and trapping it in the system . As the " Malevolence " desperately tried to retreat from the battlefield , Kenobi and Yularen arrived in the system with a triad of Star Destroyers and began to attack the warship , and Grievous called in reinforcements that were intercepted near the Kaliida Nebula by Luminara Unduli . In order to force the Republic fleet to cease their fire at his warship , Grievous captured Senator Padmé Amidala — who had been tricked into traveling to the battlefield under the pretense that the InterGalactic Banking Clan wished to negotiate a treaty with the Republic — and took her hostage aboard the " Malevolence " . Though the Republic cruisers did abandon their assault on the " Malevolence " , they continued it with renewed vigor once Skywalker and Kenobi had infiltrated the " Malevolence " and rescued Amidala from being captured by Grievous . Thanks to sabotage on Skywalker ' s part , the " Malevolence " navigational computer malfunctioned when the warship attempted to flee to hyperspace and crashed into the Dead Moon of Antar . Although Grievous escaped from the battle , his deadly warship had seen its final day . Separatist bioweapons . Despite losing the Dark Reaper , the Confederacy still continued research on developing weapons . On the Techno Union world of Queyta , researcher Jenna Zan Arbor had developed a bioweapon known as the swamp gas which appeared as a green mist and caused blisters and eventually death in many humanoid races . The Separatist Commander Asajj Ventress decided to test the virus on the Gungan colony of Ohma - D ' un , a moon of Naboo . This killed all the Gungans on the moon . In response , four Jedi Knights including Obi - Wan Kenobi , Anakin Skywalker , Master Glaive and Zule Xiss were sent to investigate what had happened . To stay unnoticed , the team flew to the moon in a single LAAT / i gunship . The Jedi were soon attacked by super battle droids fitted with swamp gas sprayers along with Asajj Ventress and the bounty hunter Durge . Their escort clone troopers , along with Glaive , were slain though Skywalker , Kenobi and the ARC trooper Alpha - 17 succeeded in defeating the Separatist duo and their forces for the time being . They then destroyed the capsules of the virus that were being loaded onto ships destined for Naboo and rescued the spice miners that were to be implicated in the disaster . Zule Xiss lost her arm to Asajj Ventress during the fight but survived to fight again thanks to Obi - Wan ' s intervention . Naboo was saved , but Ventress and Durge managed to escape . Unknown to the Jedi , a second laboratory had also been established on the far side of Queyta , the Separatists had loaded its creations aboard the " Lucrehulk " - class Core Ship " Gahenna " . This vessel would roam the galaxy for the next two years , modifying the swamp gas to become the Trihexalophine1138 toxin that devastated Honoghr . Naboo would again be involved in stopping another Separatist bioweapon , the Blue Shadow Virus , later that year : The Jedi Council sent Kenobi , Skywalker and Ahsoka Tano to Naboo in response to intelligence that suggested that a Separatist bio - lab had again been set up on the planet . When contact with Senator Amidala and Representative Jar Jar Binks , who had begun the search for the lab , was lost , Skywalker sent Tano along with the Gungan native Peppi Bow to locate them . Meanwhile , Skywalker and Kenobi learnt from information discovered by Gregar Typho that Separatist scientist Nuvo Vindi was using the lab to perfect the deadly Blue Shadow Virus so as to release it into key Republic star systems . While Tano and Bow searched the swamp where Binks and Amidala disappeared , they accidentally found a spy camera . While hiding from the spy camera , Tano contacted Skywalker and Kenobi who told her to detonate a bomb in the south bunker to create a distraction . After this , Kenobi entered the lab and aided Tano , before beginning a search for Vindi ' s virus bombs . Though Vindi attempted to release the virus , the Jedi were ultimately able to apprehend him and rescue Amidala and Binks . When Kenobi and Skywalker prepared to transfer Vindi for trial , Tano , Amidala and several clones went about further securing the lab , only to discover that a vial of the virus was missing . Though they were able to sound the alarm , it was not in time , and Vindi ' s still at large personal assistant droid was able to detonate a bomb releasing the virus throughout the lab . The Jedi were then forced to make their way to the planet of Iego to search for the antidote to the virus , so as to save Amidala and Tano . While on Iego , the Jedi were able to free the people there from an insidious Separatist weapon designed to prevent the inhabitants from leaving the planet . They were also able to locate the antidote and arrived in time to save Tano and Amidala . A third attempt at bioweapons by the Confederacy in the first year of the war was the development of a nanovirus by Ovolot Qail Uthan , designed to kill clone troopers by targeting their identical DNA . The clone commandos of the Special Operations Brigade ' s Omega Squad were deployed to destroy Uthan ' s lab on Qiilura after the Jedi Order lost contact with Jedi Master Kast Fulier . With the aid of Fulier ' s Padawan Etain Tur - Mukan , Omega Squad destroyed the facility and took Uthan into Republic custody . Separatist leadership targeted . The capture of Nute Gunray . A diplomatic mission in the first year of the war involved Senator Padmé Amidala of Naboo going to Rodia in an attempt to persuade Senator Onaconda Farr , a close family friend of hers , to keep his allegiance to the Republic . Upon arrival , she learnt that Farr had already pledged allegiance to the Separatists because of their supply offerings to the impoverished planet . Already , there were battle droids in his city . Amidala was promptly arrested and jailed but managed to escape . Nute Gunray arrived and used the threat of no supplies as leverage to have Amidala ' s execution ordered . Fortunately , her droid C - 3PO managed to send out a message before being captured . However , Amidala was cornered and just about to be executed when Jar Jar Binks arrived and rescued her . Farr arrested Gunray , revealing the entire operation had been a ruse designed to capture him , and the Republic moved in vowing supplies and support for Rodia . Viceroy Gunray was transferred to the " Tranquility " under Jedi Master Luminara Unduli where he was to be carefully taken to Coruscant to face war crimes . Ahsoka Tano and a number of Senate Commandoes under Captain Faro Argyus had also been transferred to ensure the Viceroy ' s safe arrival . Though Ahsoka didn ' t believe that all the extra security was necessary , Luminara maintained that the Neimoidian was more dangerous than he was worth . Elsewhere , Sidious reminded Dooku that Gunray was essential to their war efforts . Dooku suggested sending Asajj Ventress to reclaim the Viceroy , despite her previous failures , recognizing her talents . Back on the " Tranquility " , Unduli and Tano interrogated their prisoner . When they seemed to have little success and the Viceroy supplied evasive answers , Tano threatened him only to be chastised by Unduli . Unfortunately , a swarm of droid fighters escorting three Separatist boarding ships attacked the " Tranquility " before the interrogation could resume . Super battle droids lead by Ventress infiltrated the cruiser , while Unduli went to deal with the droids , leaving Tano to guard Gunray . Ventress planted a number of thermal charges on the cruiser ' s generators before going to the brig . She dueled Tano for a short while before ironically locking her in Gunray ' s cell . Luckily , Unduli ' s timely arrival prevented Ventress from rescuing Gunray . Unfortunately , she detonated the charges , rocking the ship before fleeing down the elevator shaft . Unduli went after Ventress , confident that she could defeat the assassin , leaving Tano alone again . Argyus advised Tano to do what she thought was right . In the generator room where the duel had proceeded , Ventress outclassed Unduli , pinning her down with pipes . Tano made a timely entry , saving the Jedi Master ; only for Ventress to escape again . Back in the brig , Argyus betrayed his fellow commandos , revealing that he was bribed by Dooku . Commander CC - 1004 managed to overpower him only to be knocked out by Gunray . They made their escape on the docked Republic ship in the lower hangar , joined by Ventress , who used an escape pod . Argyus gloated that he would take most of the glory , but Ventress stabbed him in the back . Later , Tano and Unduli reported to Yoda and Skywalker about the loss . Luckily , as the stolen ship belonged to the Republic , it could be tracked . Tano left to join Skywalker with Kit Fisto ' s fleet , but not before receiving an apology from Unduli for not listening to her . Once alerted of Gunray ' s escape , Jedi Master Kit Fisto and his former apprentice Nahdar Vebb followed the tracking beacon of his stolen ship to Vassek , but soon found that he was not there . They attempted to sneak up on him , but all they found was a gloating hologram . It turned out to be a trap for them and a test for Grievous , who had received a holo message from Count Dooku , telling him that Darth Sidious wanted more results — dead Jedi . Upon his arrival to his lair , Grievous was confronted by Fisto and Vebb , along with their squad of clones . A lightsaber duel broke out and Grievous ended up having his legs chopped off just above the knees . However , Grievous escaped to his control room where he underwent repairs from his medic droid . Grievous then ordered his MagnaGuards to blow up the clones ' transport , which killed at least two clones . They attempted to destroy Fisto ' s starfighter and his droid , R6 - H5 , also , but R6 - H5 managed to pilot the fighter away from danger . Meanwhile Fisto , Vebb and the remainder of their clone squad followed Grievous , finding many booby traps along the way . A trapdoor fell from beneath them , and one of the clones was killed in the lava pit below . Fisto and Vebb Force Jump ed above the pit , and Clone Commander Fil used a cable to cling to the side of the pit and climb up . After this debacle they met Grievous ' s pet roggwart , Gor . After a short battle , Gor was eventually killed by Fisto . Unfortunately , Fil was killed which enraged Vebb . While Grievous was watching this all play out , he was contacted by Count Dooku . This time the message confirmed to Grievous that this was a test for him . He decided to play along , and he and five of his guards went hunting . When the two parties met up , Vebb skillfully defeated all five of Grievous ' s guards . During the fight , Fisto was locked into the control room , unable to help Vebb . Vebb proceeded to attack Grievous , but was shortly shot and killed by Grievous . Fisto called for R6 - H5 to meet him at the south landing platform . After a brief but intense battle with Grievous , Fisto escaped and returned to the Jedi Temple on Coruscant , where he told Yoda and Mace Windu about the confrontation . He told them that Vebb ' s heart was in the right place , but he tried to match Grievous ' s power with his own . Dooku proved pleased with Grievous ' s achievements ; though he noted that the cyborg general ' s failure to kill Master Fisto was evidence enough that he had much to improve upon . Dooku captured . Sometime after the debacle on Vassek , Jedi Generals Obi - Wan Kenobi and Anakin Skywalker spearheaded an attempt to capture the head of the Confederacy ; Count Dooku himself . While the Jedis ' attempts to capture the Count aboard his flagship proved unsuccessful , Ahsoka Tano successfully commanded a Republic force against it , forcing Dooku to crash land on Vanqor during his escape from the doomed vessel . While Kenobi and Skywalker searched for the Count in a cave nearby to the wreckage of his personal craft , Dooku used the Force to cause a roof collapse ; trapping the Jedi and securing his escape . After making contact with a nearby group of pirates , Dooku secured himself a route off - world ; only to find himself captured by the wily gang of pirates who hoped to trade him for a hefty ransom from the Republic . After being rescued by Tano , Kenobi and Skywalker were sent to the pirates stronghold to ensure they had indeed captured Dooku , and after he received confirmation from him , Chancellor Palpatine had Representative Binks and Senator Kharrus lead a diplomatic mission to trade a ransom for the Count . The pirates proved treacherous , however , and captured Kenobi and Skywalker hoping to gain an additional ransom for them . Fortunately , Representative Binks was able to rescue them ; though the mission did come at the cost of Senator Kharrus ' life , and Dooku managed to yet again evade the clutches of the Republic . Year two ( 21 – 20 BBY ) . The war in the Core . The capture of Brentaal IV . The second year of the war was characterized by Separatist gains and Republic embarrassments , bringing the war into the Core Worlds itself . The Republic Loyalist world Kuat and the Separatist world Neimoidia seeded the hyperlanes between them with mines , effectively rendering the heart of the Hydian Way impassable . Brentaal IV sat at the crossroads of the Hydian and the Perlemian Trade Route , the galaxy ' s two most vital super - hyperroute s , controlling access to the Core and the Rim and of incalculable importance to the Republic . However , outside the planet ' s noble houses and trade guilds , the people of Brentaal ached for a new life under the CIS . Brentaal clan leader Shogar Tok incited his people to riot against the Republic - friendly planetary government . Jedi Master Plo Koon led the counterattack on the planet , overseeing a task force of three Jedi and a strong complement of clone troops and support vehicles . However , Tok ' s mercenaries had already taken control of Brentaal IV ' s defenses , forcing a chaotic battle that saw the capture of several Jedi by the Separatists until they were able to escape their imprisonment and destroy the planet ' s shield generator , allowing Plo Koon to land and secure Brentaal . The Bassadro massacre . A series of events at this time caused significant changes in wartime politics and led to an increase in security and propaganda on both sides of the conflict . On Bassadro , Jedi Knight Empatojayos Brand led his forces to the dormant volcanic ranges that were providing cover to Separatist droids . Brand ordered concussive missile strikes against the rock formations , creating a storm of shrapnel that sliced through the mining village of Agao - Nir , destroying many droids and several hundred innocent miners . The public outcry from this incident impacted both sides — the Confederacy , in response , founded the Hyper - Communications Cartel to broadcast anti - Republic propaganda , while the Republic formed the fanatic pro - Human COMPOR and SAGroup and instituted deportation of ' enemy ' species from Coruscant . During an assault on Coruscant , Count Dooku and his dark acolyte Trenox infiltrated the capital world with a small force of C - B3 cortosis battle droid s and attempted to destroy the Jedi Archives in the Jedi Temple , but fled after Anakin Skywalker arrived on the scene and defeated Trenox in a follow - up from a mission on Tatooine . This battle , coupled with the blackout on Sarapin , made many of Coruscant ' s citizens feel unsafe and security increased even further . Huge stretches of the cityscape were transformed into military staging areas and clone troopers were on patrol everywhere . Jedi Generals Etain Tur - Mukan and Bardan Jusik led Omega Squad , Delta Squad , and a unit of Null ARC troopers in a purge of a Separatist terrorist group along the skylanes and underworld of the ecumenopolis . Following increased threats to Coruscant in the wake of the Battle of Jabiim , a special batch of clone troopers known as the clone shock troopers were raised and trained on Coruscant itself , rather than Kamino , where they became a familiar sight , operating as martial police . Preying on citizen ' s fear , Palpatine founded the War Council Advisory Panel and the Homeworld Security Command . The Northern Campaign . Continued raids . At the time of the Haruun Kal Crisis , Obi - Wan Kenobi and Anakin Skywalker were sent to Null after they received information from Lorian Nod about a meeting arranged by Dooku with the rulers of Vicondor , Delaluna , Bezim , and Junction V . Unfortunately , there was an assassination attempt on Samish Kash , ruler of Delaluna . Kenobi and Skywalker took off after the assassin on speeder bikes but were unable to stop it . Soon , after Dooku arrived they discovered that it was he who hired the assassin , a man named Robior Web . During the meeting the rulers chose to support the Republic . Dooku was furious , and trapped the delegates by making the roof cave in on top of them . However , all survived with the help of the Jedi , save for Nod , who was killed by Dooku . Dooku then escaped . On Nadiem , General Grievous attempted to invade a major city , but was forced to retreat after Jedi Luminara Unduli and Barriss Offee herded his droid army into a canyon and set off explosive charges that crushed the droids under the crumbled canyon walls . Clone commandos were sent to Ord Mantell after Trandoshan bounty hunters intercepted an important package that had been sent to Supreme Chancellor Palpatine from Malastare diplomats . Two squads of Republic commandos were sent to Ord Mantell to retrieve it before the bounty hunters could sell it to the Separatists . On Ord Mantell , the clones located and engaged the bounty hunters , but Blue Squad was killed when the Trandoshans struck back with thermal detonators . White Squad tracked the bounty hunters as they attempted to flee , and destroyed a number of battle droids sent to retrieve the object , though one of the squad members fell to droid fire . When the squad finally confronted the Trandoshan bounty hunters , a firefight ensued in which two more commandos and all but the Trandoshan ' s leader were killed . White Squad ' s sergeant and only surviving member , RC - 1013 , jumped onto the final bounty hunter as he attempted to flee , killing him , and recovering the package for the Republic . When a Separatist fleet blockaded Balamak , an important agricultural world , Generals Obi - Wan Kenobi and Nanda - Ree Janoo led a Republic strike force of starfighters , while Anakin Skywalker engaged a Trade Federation Droid Control Ship carrying a HoloNet jamming device that had blacked out sector communications since the arrival of the fleet . The jamming vessel was destroyed and the Separatist fleet was routed in the battle . Meanwhile , the new " Katarn " - class commando armor had just been issued to the Commando squad Omega to be used on a mission to eradicate a phrik factory on Fest . Shortly after the Battle of Jabiim , Jedi Knights A ' Sharad Hett , Bhat Jul , and Anakin Skywalker were sent to Aargonar to repel a Separatist presence . The battle was a disaster , and Jul and many clone troopers were slaughtered . Ki - Adi - Mundi gave the order to retreat , while Bultar Swan was tasked with destroying the Republic camp to keep supplies from falling into the hands of the enemy . Meanwhile , Anakin and Hett , who had gone into a cave to hide , found a disabled gunship and used it to lure a Gouka dragon into the Separatist forces , giving the Republic time to retreat . The Jedi then returned to New Holstice . Anakin Skywalker led a strike team to liberate the planet Virujansi and , after having done so , the grateful natives dubbed him their " warrior of the infinite " . However , the Republic suffered another loss when Togoria seceded , giving the Confederacy a route to the strategic hyperspace crossroads of Kashyyyk . The Battle of Jabiim . The Republic ' s minor successes in the northern theatre would be completely undone by the disastrous Battle of Jabiim . The Outher Rim world of Jabiim lay within the Republic Twelfth Army ' s theatre of operations on the Triellus Trade Route trailing of Centares . The Twelfth Army had had a good early war , advancing quickly from its secure rear base at Lantillies to Centares , eroding the northern flank of Confederate territory on the Hydian Way . The rapid advance , however , completely ground to a halt in weeks of warfare on Jabiim , despite the death of Confederate leader Alto Stratus . From the outset , the Republic encountered generally poor conditions on the planet - the ground was muddy and the clone troopers could not count on air support due to electrically charged atmospheric disturbances . Instead , they relied on a strong mechanized ground assault , led by the newly produced AT - AT walkers . The Jabiim Separatists , however , having lived amidst the rain and mud , were much better suited for combat . In the second week of the battle , they routed the Republic ' s Shelter Base and captured the commanders Obi - Wan Kenobi and ARC trooper Alpha - 17 . The two were subsequently moved to Rattatak . Although Anakin Skywalker led a force of Padawans in a counterattack that resulted in the death of Stratus , the Republic would ultimately be forced to cede the planet to the Confederacy . Hunt for General Grievous . Jedi Master Eeth Koth ' s Star Destroyer was assailed by a fleet of warships led by Grievous and was subsequently boarded by the general and his battle droid forces . While super battle droids engaged clone troopers commanded by Captain Lock on the cruiser ' s lower levels , Grievous made his way to the bridge alongside a contingent of droid commandos and IG - 100 MagnaGuards . The droid commandos killed all of the bridge ' s defenders with the exception of Master Koth , who was soon defeated and taken captive by Grievous and his MagnaGuards . Koth was later displayed as a hostage in a transmission sent by Grievous to the Jedi High Council in which he brutally tortured Koth to express his hatred for the Jedi Order . Koth used discreet hand signals to inform the Council of his location and Kenobi , Adi Gallia and Skywalker , organized an assault force to engage the Confederacy at Saleucami , rescue Koth , and capture General Grievous . Kenobi was the first of the Jedi to arrive at Saleucami and engaged Grievous ' s forces with a fleet of Star Destroyers and nimble " Consular " - class frigates under the command of Admiral Yularen . Kenobi ' s light cruiser was caught in a tractor beam from Grievous ' s Separatist destroyer and was boarded . While Grievous was dueling Kenobi , Skywalker and Gallia infiltrated the General ' s destroyer to rescue Eeth Koth . Meanwhile , Grievous , understanding that Kenobi had the upper hand in their duel , retreated to his destroyer and led his battle droids onto a landing craft bound for Saleucami ' s surface . During the descent , the craft collided with debris from the battle , forcing Grievous to flee the doomed vessel in an escape pod . While Skywalker continued the battle in orbit , Kenobi led a force of clones to the planet ' s surface to hunt down Grievous . The cyborg General evaded and fled from the Republic forces , hoping to call for an evacuation transport . Captain CT - 7567 was seriously injured , necessitating aid from local farmer Cut Lawquane , a clone who had deserted the Grand Army . Meanwhile , Kenobi caught up with and engaged Grievous , who fled the battle once a " Sheathipede " - class shuttle arrived to ferry him away . Mandalore and the Death Watch . The Council of Neutral Systems was formed as a reaction to the war , composed by systems who did not wish to join the conflict . The leader was Duchess Satine Kryze of Mandalore , head of the pacifist New Mandalorians . The Separatists offered help to the Death Watch in Governor Pre Vizsla of Concordia ' s fight against Kryze ' s reformation and at taking over the Mandalorian government . Mandalorian Supercommando s performed sabotage missions for the Separatists against Republic targets , such as when a commando attempted to sabotage a Republic cruiser who then committed suicide . These events in addition to falsified rumors led to the Republic ' s belief that Kryze , was training a Mandalorian army for the Separatists . The Republic ' s Tenth Army moved to guard against further Separatist diplomatic efforts in the region , while General Kenobi was sent to Mandalore to investigate when Kryze revealed the existence of the Death Watch . While he was there , Vizsla communicated with Dooku who revealed his strategy for the Republic to establish peacekeeping forces on Mandalore . Dooku hoped this would cause unrest and lead the Mandalorian populace to join the Death Watch . On their way to Coruscant and on board the starship " Coronet " , Kryze , Kenobi and Skywalker were attacked by three assassin probe s programmed by New Mandalorian Senator Tal Merrik had programmed them to kill the Duchess . With Droch - class boarding ships , droid forces boarded the ship but were destroyed by Skywalker and his troops and Kryze was freed from Merrik ' s hold . On Coruscant , Palpatine quickly ruled that the Death Watch was a military threat to which Kryze objected . During her stay the Death Watch reoccupied their base on Concordia as a staging area for their impending invasion of Mandalore and Vizsla made his move to secure Mandalore ' s support to Dooku . A Death Watch assassin attempted an assassination against Kryze which was ruled out as an accident . She and Kenobi however deduced that it was also an attempt to start a war with Mandalore . The Senate had passed the vote for occupation behind her back , based on a forged holorecord by Deputy Prime Minister Jerec . Later Kryze received the original message and let Kenobi deliver the unaltered holo to the Senate . Obi - Wan showed the message and the decision to invade Mandalore was scuttled which compelled Death Watch to cease its planned attack . The Southern Campaign . The Eriadu Salient . With much of the Rimward end of the Rimma Trade Route in Separatist hands , Eriadu and Sullust had served as significant Republic bastions against CIS forces moving from Sluis Van and Clak ' dor VII . Just over a year after the Battle of Geonosis , however , Sullust seceded from the Republic owing to its ties with the Commerce Guild . Additionally , Sullust had been worried by Eriaduan expansionism and militarism since the days of Ranulph Tarkin , nearly thirty years earlier , which had pushed it even closer towards the Confederacy . With Sullust in the Confederacy ' s fold , Republic Loyalist worlds along the Rimma Trade Route , including Praesitlyn and the hyperspace crossroads of Eriadu were left in a vulnerable salient in Confederate space . In response , the Republic heavily - fortified the Eriadu base . Brigadier Gideon Tarkin and his brother , Wilhuff Tarkin , who became one of the first Moffs , organized the defense . Brigadier Tarkin merged various planetary navies into priority theaters and commanded them from Eriadu . Besieged on all sides , the operations of the Seswenna sector ' s Eighteenth Army and Republic Outland Regions Security Force were heavily propagandised and made heroes out of Tarkin and his army . Ultimately , betrayal in the Republic ranks led to their defeat at the Battle of Sullust , but the overall campaign led to the Republic ' s recapture of part of the Sluis sector , assisted by the Sons and Daughters of Freedom . Continued raiding . Obi Wan Kenobi and Anakin Skywalker assisted in the destruction of a droid factory at Nivek before going on to retake Terra Sool . Simultaneously , Republic forces led by Jedi Masters Mace Windu and Saesee Tiin liberated Iktotch at the Battle of Iktotch . Raiders associated with the Separatists had been attacking Republic convoys on the Corellian Trade Spine including five which hailed directly from Coruscant . The raiders ' tactic was to use a gravity well to pull the ships from hyperspace and into an ambush for which the craft were unprepared . This led to a series of skirmishes . The fates of the crews are uncertain but one known casualty was Elsah ' sai ' Moro , who , having contacted the Jedi Council and told it of the loss , died shot down by the bounty hunter Aurra Sing . On Devaron , a Jedi task force consisting of Kit Fisto , Aayla Secura , the An ' ya Kuro , Tholme and T ' ra Saa arrived to halt a smuggling operation that Aurra Sing and Senator Vien ' sai ' Malloc had started . Sing was captured and imprisoned at the Oovo IV asteroid prison , though she would manage to escape . On Antar 4 , Antarian Separatists backed by Count Dooku overthrew the Jedi - allied Antarian Rangers that enforced law on the moon , while , on Nar Shaddaa , Quinlan Vos succeeded going deep behind enemy lines , convincing most of the Jedi Order that he had betrayed them and defected to the Separatists and joined Count Dooku ' s cadre of dark acolytes , but he was really on a top secret mission to gather intelligence for the Jedi High Council . During a mission to the Chaykin Cluster , Delta Squad liberated the " Acclamator " - class assault ship " Prosecutor " from Trandoshan mercenaries aligned with the Separatists . On Parcellus Minor , the Separatists routed Republic defenses at the cost of igniting the flammable native plants through a wave of orbital bombardment and starting a fire that spread to much of the surface , wiping out or injuring most of both the ground forces on both sides . Following their capture at the Battle of Jabiim , Obi - Wan Kenobi and the ARC trooper Alpha - 17 were interrogated and tortured by Asajj Ventress on Rattatak , though they managed to resist . In response , she fed Kenobi muscle maggot s that ate away his strength and also placed him in a Sith torture mask to stifle his Force presence . He overcame it , however , and though it took nearly a month , Kenobi managed to slowly bend the water pipes in his cell and free himself , Alpha , and the other prisoners . They repelled a final confrontation by Ventress and escaped . Obi - Wan alerted Anakin Skywalker to his survival through a Force message , which the latter received while battling pirates in Ki - Adi - Mundi ' s task force . Obi - Wan and Alpha meanwhile had arrived on nearby Riflor where they fought through Ventress ' pursuers before being reinforced by Ki - Adi - Mundi and Anakin . The Blockade of Pantora was set up by the Trade Federation to force the Pantoran Assembly to join Count Dooku and the separatist ' s . To force Chairman Notluwiski Papanoida to join the Trade Federation hired two Bounty Hunters to kidnap his daughters . It ended when Jedi Padawan Ahsoka Tano and Pantoran Senator Riyo Chuchi rescued one of them while Chairman Papanoida and his son Ion rescued the other . The Second Battle of Geonosis . Following a mission to Cato Neimoidia , the Republic discovered a new droid foundry on Geonosis , which had been thought abandoned since the start of the war . To distract the Republic from a new attack on Geonosis , General Grievous struck at the Kel Dor homeworld of Dorin . Although the Kel Dors suffered in the defense of their planet and initially began to be overwhelmed by Grievous ' s battle droid troops , a large Republic fleet under the command of Jedi Generals Plo Koon and Anakin Skywalker , Admiral Wullf Yularen , and Jedi Commander Ahsoka Tano arrived to reinforce Dorin . In the subsequent naval engagement , the Jedi and their clone trooper starfighter squadrons were able to turn the tide against the Separatist assault fleet , forcing a Confederate retreat from Dorin . While his remaining forces were routed by the Republic , Grievous managed to escape from the battle in his personal starfighter . In the aftermath of Dorin , the Republic launched a full - scale planetary invasion of Geonosis to shut down the droid factories . The Second Battle of Geonosis proved to be a hard fight . Tasked with the challenge of landing on the planet and establishing a staging area , the Jedi mounted a three - pronged attack on the Geonosian defenses in what became known as the " Battle of Point Rain " , with Jedi Generals Ki - Adi - Mundi , Obi - Wan Kenobi , and Anakin Skywalker each leading an assault force . After establishing a landing zone at Point Rain , the Republic army regrouped and disabled the factories ' ray shields , making way for the rest of the clone trooper forces to safely land . In order to eliminate the factory , Generals Skywalker and Luminara Unduli battled the facility ' s droid defenses in open warfare while their respective Padawans , Ahsoka Tano and Barriss Offee , sneaked into the facility via the catacombs beneath it . Tano and Offee used a super tank to blow up the facility ' s reactor and collapse the factory from the inside . A hunt for Archduke Poggle the Lesser and the Geonosian Queen Karina the Great ensued in the aftermath of the battle . The Jedi and their troops destroyed much of the queen ' s lair during their escape , killing Karina the Great and burying her warriors beneath the temple , and the Republic ' s recapture of Geonosis was secured . The Second Battle of Kamino . Several months after the destruction of Rishi Station , Grievous and Ventress planned another assault on Kamino . Skywalker and Kenobi caught wind of their plan when they had intercepted a coded message between Grievous and Ventress . They immediately rushed over to secure the clone planet . While Grievous arrived with a fleet to challenge the Republic ' s fortified blockade of Kamino , he secretly led Trident drills down to the surface by disguising them as debris from the space battle and having them crash into Kamino ' s oceans to join Ventress , who was already down there with her ship . Once the assault craft were assembled , they rose out of the oceans and deployed their forces to attack Tipoca City . While General Shaak Ti led the clone troopers to defend the city ' s Military Complex , Skywalker intercepted Ventress , who had stolen the clones ' DNA template , while Kenobi dueled Grievous at the clone barracks . Both duels moved outside , and though Ventress and Grievous escaped , Skywalker managed to retrieve the DNA , and Ti was able to drive the droid forces away , thwarting the Separatists ' invasion of Kamino and securing the key world . Further weapons development . The Planet Killer . Master Mace Windu undertook a covert operation to an Omphalos to disable a Separatist superweapon developed by its designer known as the " Planet Killer " . Originally arriving in an LAAT infantry transport with a force of clone troopers , the transport was spotted by Separatist forces and shot down , leaving Windu as the only survivor . After fighting his way through numerous battle droids , Windu located the Planet Killer and disabled it by destroying its detonator . The Cortosis Battle Droids . The Jedi High Council received a disturbing report from an informant named Raala Ponchar of a new type of battle droid being seen on Tatooine . Not long after delivering this report , Raala disappeared . Anakin Skywalker was sent in to investigate and discovered a womp rat infestation that was plaguing Mos Espa . Investigating the infestation , Anakin investigated the womp rat nests in the Xelric Draw and eliminated anoobas that were flushing the womp rats out of their nest . As Anakin left the nests , he encountered Aurra Sing , who revealed that she had been behind the entire problem as a distraction in order to orchestrate a bounty placing on Anakin by Jabba the Hutt . Now having to contend with bounty hunters in both Aurra and Jabba ' s employ , Anakin returned to Mos Espa to interrogate his former slave owner , the Toydarian junk dealer Watto , about information on Raala ' s whereabouts . Watto directed Anakin to a Dune Sea moisture farm and interrogated a farmer named Bellek , who in - turn directed Anakin to Jabba ' s palace . While crossing the Dune Sea and the Jundland Wastes , Anakin encountered several of the battle droids mentioned in Raala ' s report to the High Council . When Anakin reached the palace , he confronted Sing once again , but before he could apprehend her , a dark acolyte named Saato arrived and Force choked Anakin into unconsciousness . Upon waking up , Anakin was in a cell in the palace dungeons with Raala . Raala informed Anakin that the Separatists had hired Jabba to transport a lightsaber - resistant metal called cortosis so they could use it to construct new droids . After breaking out of the dungeon , Anakin obtained a skiff and escaped the palace ; however , Saato also obtained a skiff and pursued Anakin , eventually shooting him down near the Great Pit of Carkoon . Saato and Anakin soon engaged each other in a lightsaber duel , with Anakin emerging victorious when he knocked Saato into the Pit , causing her to be eaten by the Sarlacc . In the aftermath of both the investigation on Tatooine and the attack on Coruscant , the Jedi Council sent Anakin Skywalker to Metalorn to capture Wat Tambor , the Foreman of the Techno Union and a high - ranking member of the Separatist Council in order to stop the creation of the cortosis battle droid army . While searching for Tambor , Anakin was confronted by two dark acolytes : the brothers Vinoc and Karoc . After defeating them in a lightsaber duel , Anakin eventually reached the factory power core . He planted a series of bombs and then continued his search for Tambor . He eventually found him , and after defeating his bounty hunter bodyguard Vandalor , captured him . He then made it out of the facility before it exploded . He also killed a doppelgänger of Count Dooku that tried to convince Anakin to give into the Dark side of the Force . Tambor was turned over to Supreme Chancellor Palpatine , who had him imprisoned in the Republic ' s prison facility on Delrian . However , this imprisonment would not be permanent ; members of the Commerce Guild would rescue him during a Separatist - conducted raid . The Spaarti Incident . The planet Cartao in the Prackla sector had remained unaligned in the war thus far , but it was the headquarters of Spaarti Creations , a company whose unique method of manufacturing would draw the eyes of powers eager for new weapons . By using a " fluid retooling " process unique to their species , the native Cranscoc could adjust the Spaarti factory overnight to produce virtually any product . Both the Separatists and Supreme Chancellor Palpatine saw the usefulness of such technology for their respective war efforts , the former to produce a new type of battle droid , and the latter for the company ' s Spaarti cloning cylinder s , which could be used to grow battle - ready soldiers in less than a tenth of the time it took the Kaminoans to produce the same . In several weeks of fighting on Cartao , the Spaarti factory changed hands a number of times . The facility was eventually destroyed by a Low Altitude Assault Transport gunship crashing into the complex , an incident that the Jedi were implicated in , but denying the factory to the Separatists . However , through his agent Kinman Doriana , Palpatine had secretly acquired thousands of cloning cylinders for the Republic . These were sent to Byss , Wayland , and Centax - 2 , a moon of Coruscant where millions of new clones were grown in secret . This " secret army " was ready to be unleashed in the war ' s final year , and was instrumental in grinding the Separatists down in the Outer Rim Sieges and driving them from the Coruscant system in the final stages of the Battle of Coruscant . Year three ( 20 – 19 BBY ) . The war in the Core . Operation Durge ' s Lance . The Republic ' s war effort reached its nadir when General Grievous launched Operation Durge ' s Lance . Driving from Yag ' Dhul and Thyferra , two Confederate fleets advanced into the Core Worlds , and after several weeks of campaigning , had reached Duro . Separatist warships destroyed the defending Republic fleet and captured one of the planet ' s orbital cities in less than a week . This was followed by a wave of orbital bombardments and the landing of a massive droid army on a conquered Duro . Following the battle , the Senate Bureau of Intelligence investigated causes of the defeat . A month later , in a report issued by Agent Inglemenn Barezz , it was revealed that the three " Venator " - class Star Destroyers that were to have been assigned to protect Duro had been reassigned to " shakedown cruises " by the Senate Action Subcommittee for Corellian Trade Spine Defense . Having conquered Duro , Grievous continued his rampage throughout the Core , wreaking havoc along the Corellian Trade Spine . From the bridge of his flagship " Invisible Hand " , he supervised attacks on 26 strategic Loyalist worlds . Among his atrocities , Grievous was responsible for an hour - long orbital bombardment which depopulated and melted the crust of Humbarine , an ancient city world and Core Founder . Another Core Founder , Kaikielius , was occupied by Confederate forces . At Loedorvia , he unleashed the Brainrot Plague into the Weemell sector , killing most of the Sector ' s Human inhabitants . On Vandos and Nadiem , civilians and soldiers alike were massacred on his orders . Grievous also collected the lightsabers of Jedi fallen by his blade as trophies of war . Due to these acts of wanton destruction , Grievous soon became an avatar of terror in the eyes of the citizens of the Republic . The Foerost Siege . With Grievous raiding throughout the Core , Separatist forces besieged at Foerost took this opportunity to break out . The ancient shipyards at Foerost in the Deep Core had been churning out warships for millennia . Toward the last centuries of the Republic , the Techno Union had purchased the Foerost shipyards . With the advent of the Clone Wars , Foerost was blockaded by the Republic Navy in the hopes that the starved shipyards would wither and decay . But the Republic was unaware that for two years after the Battle of Geonosis , the besieged Techno Union engineers had been designing the Bulwark Mark I — a 1 , 000 meter - long warship equipped with powerful weapons and enough armor for ramming smaller vessels . Under the command of the Sullustan Admiral Dua Ningo , the Bulwark Fleet smashed through the Republic blockade at Foerost and proceeded to terrorize Republic worlds within Sector Zero . In response to the Bulwark Fleet , the Republic launched its " Victory I " - class Star Destroyers six months early . The product of the Victor Initiative Project between Kuat Drive Yards and Rendili StarDrive , the " Victory " - class warships formed the Victory Fleet and were divided into two task forces led by Captain Terrinald Screed and Jan Dodonna . They saw action against the Bulwark Fleet at Ixtlar , Alsakan and Basilisk . At the Battle of Anaxes , Ningo was killed and his fleet finally defeated . Screed and Dodonna would return to Coruscant as heroes for the Republic . The Dreadnaughts of Rendili . The Core World of Rendili , a major starship producer , voluntarily defected to the Separatists . Its defense fleet was composed of the then state - of - the - art " Dreadnaught " - class Heavy Cruisers . However , the fleet commander had not yet decided which side he was on . In response , a Republic fleet under Jedi Masters Saesee Tiin and Plo Koon arrived with orders to destroy the " Dreadnaught " cruisers if they refused to join the Republic . However , during the negotiations , Plo Koon and Captain Jan Dodonna became the prisoners of a group of pro - Separatist officers in the " Dreadnaught " fleet led by Lieutenant Mellor Yago . Yago hoped to break the Republic blockade with these hostages . However , Saesee Tiin refused to back down . Soon , Obi - Wan Kenobi and Quinlan Vos arrived , having just escaped from Asajj Ventress . Since Quinlan Vos had failed to obtain the SIP from Honoghr , Count Dooku wanted him dead and his role as a double agent was over . Both Jedi rescued the hostages from the " Dreadnaught " cruisers before engaging Separatist fighters . Meanwhile , Anakin sabotaged the " Dreadnaught " s to prevent their escape into hyperspace . During the battle , Yago was slain by Jace Dallin . With the end of the battle , the captured " Dreadnaught " s were modified into prisoner transports and Supreme Chancellor Palpatine made a new law that nationalized all similar , planetary - level defense fleets . Meanwhile , Quinlan Vos appeared before the Jedi Council and admitted he had joined the Dark Side during his time with Dooku and presented himself for sentencing . However , the Council agreed to allow him to rejoin the Order after he had endured a period of meditation and repentance . However , he was still secretly serving Count Dooku . Meanwhile , a vengeful Asajj Ventress slipped into the galactic capital Coruscant and tried to kill Anakin Skywalker in retaliation for Kenobi escaping her at Rattatak . During that battle , which took place on an industrial catwalk high above the skyscrapers of Coruscant , she scarred Skywalker ' s face with her lightsaber . However , Skywalker won the fight and then used the Force to hold her high above the surrounding metropolis and then throw her down , presumably killing her . However , Ventress survived and managed to escape Coruscant . The Northern Campaign . Drongar and Bota . By this time , many on both sides of the conflict had died and many more were injured . In response , the Republic began deploying MedStar Frigates which escorted Republic fleets into combat and carried mobile field hospitals known as Republic Mobile Surgical Unit s or RMSUs ( " Rimsoos " ) . It was amid this medical crisis that Drongar , a primordial planet of tropical climates and monsoons , with the most advanced plant life being varieties of fungi , became significant , One such Drongar growth was bota , an " adaptogenic " which worked as an antibiotic , a painkiller , or even an intoxicant , depending upon the species . Having realized its importance , and that bota deteriorated quickly after picking , both sides maintained harvesting operations on Drongar and battles were fought over the bota fields . It was here that Jedi Padawan Barriss Offee arrived to practice her skills as a Jedi healer , and discovered that bota enhanced her Force powers . Offee ' s co - workers at Rimsoo Seven were , among others , the protocol droid I - 5YQ , a young surgeon named Jos Vondar , and a Sullustan HoloNet reporter named Den Dhur . She discovered that Admiral Tarnese Bleyd , commander of the local MedStar , was profiting from a bota smuggling ring . Though he was stopped , the Republic operations on Drongar continued to be harassed by the Confederacy , which continually attacked their bota fields until the intervention of a " Venator " - class Star Destroyer ended the hostilities . Later , Offee returned to Coruscant and was promoted to the rank of Jedi Knight . The devastation of Honoghr . Included among the many tragedies of year three was the devastation of the planet Honoghr . A Republic force under Aayla Secura ' s command engaged the Separatist Core Ship " Gahenna " in orbit of the planet , forcing it to crash land on the surface . Unfortunately , the ship still carried the deadly toxin Trihexalophine1138 , which spread across the entire planet and dramatically damaged its ecosystem , leaving little plant life except for plains of kholm grass . It was also here that Aayla Secura and Commander CC - 5052 attempted to recapture the Scientific Instrument Package aboard the " Gahenna " which had been captured by the native Noghri and kept in an ancient Rakata n temple . Meanwhile , the traitor Quinlan Vos attempted to retrieve the SIP for Dooku . However , Quinlan failed when Aayla made him realize that his obsession with hunting the second Sith might not be worth the choices he had made earlier . Doubting himself ever since he had joined Dooku , he left Honoghr empty handed though it was changed forever . Republic terrorism . During the conflict , the Republic had caused grief for many inhabitants of the galaxy on several occasions , including the devastation of Orleon by stone mites . Prior to this , the Separatist scientist Jenna Zan Arbor had created stone mites — bioengineered insects that could devour buildings — with the help of Arkanian geneticists . These insects had ruined countless worlds since their introduction . On one occasion during a trip to Coruscant ' s busy Westport , the freighter " Spinner " , which had been affected by stone mites , crash - landed on Kishi . The stone mites then ravaged Kishi until Jedi healer s proficient in the art of Morichro destroyed them . Armand Isard , director of the Senate Bureau of Intelligence denounced the incident as a Separatist act of terror and his agents traced the " Spinner " to a small Mid Rim world Orleon . Believing the planet had bioweapons facilities , he unleashed Republic - altered stone mites on the planet . However , he was wrong , since Orleon had no bioweapons facilities and the stonemites destroyed much of the planet . Nothing could be done and the planet ' s 800 million inhabitants were forced to flee . The Southern Campaign . Targeting Grievous . Grievous ' atrocities in the Core prompted many Jedi to call for the cyborg General ' s assassination . However , Master Yoda opposed such extreme measures , fearing that the actions of the Jedi assassins would lead to their fall to the dark side . Despite this , some risked excommunication to carry out what they saw as justice . This included Padawan Flynn Kybo , Coway Jedi Master B ' dard Tone and a few others . This group of Jedi tracked the infamous cyborg general in the Ison Corridor . On the Ugnaught homeworld Gentes , Grievous ' s forces had conquered the planet and enslaved its inhabitants . Strip - mining also took place on the planet . He also captured a group of Padawans on Gentes and intended to make them into cyborgs though his attempts were foiled by Kybo and Tone . Uprising on Bpfassh . The suppression of a Dark Jedi uprising on Bpfassh would later be considered to be one of the turning points of the war . The Sluis sector was in a state of near - constant fighting as the Sons and Daughters of Freedom continued to attack Separatist forces in the region . The stress of the ongoing Sluis sector battles triggered an outbreak of fanatical militarism within Bpfassh ' s Jedi Praxeum , and , fully in the grip of the dark side , the Jedi there joined the Separatist - aligned Jensaarai . Bpfasshi Dark Jedi were responsible for a rampage of terror and destruction throughout the Sluis sector , setting themselves against the Sons and Daughters of Freedom before the insurrection was quelled by a Jedi task force led by Yoda . Yoda ' s task force secured the sector , but the uprising was considered a fiasco by many veterans involved , and the Bpfasshi would harbor a strong dislike for the Jedi for many years afterwards . The Outer Rim Sieges . Despite the upset of Operation Durge ' s Lance and the terror spread by Grievous throughout the Core , the Republic was at last gaining traction and now had the momentum on its side . With the Bulwark Fleet destroyed and the Rendili Dreadnaughts secured , Duro was liberated . Along with victories at Commenor , and Balmorra , this battle was instrumental driving the Confederacy from its bases in the Core Worlds and the Colonies regions of the galaxy . Meanwhile , steady pressure by the Ninth Army had cleaved Separatist holdings in the New Territories into two pieces , while the Separatist enclave on the Corellian Run Coreward of Ando had been reclaimed by the Republic . Separatist holdings on the Rimma Trade Route had also been reduced to a few enclaves around Xagobah and Yag ' Dhul . The Confederacy reinforced its Rim territories including its vast holdings on either side of The Slice . Emboldened , the Republic deployed nearly every fleet element and troop transport to the Rim in an attempt to crush the Separatist fortresses . The Republic was now able to bring its vast industrial superiority to bear to crush the Confederacy with sheer weight of numbers . Thus began the Outer Rim Sieges , which marked the final phase of the conflict . The Outer Rim Sieges were conducted in six theatres , named after the key Separatist worlds in each - Mygeeto , Serenno , Felucia , Siskeen , Yag ' Dhul and Praesitlyn . In the Praesitlyn theatre , the Nineteenth Army advanced against Bomis Koori IV , where Corporate Alliance Koorivar General Oro Dassyne commanded a Separatist fortress - city . Anticipating a massive Jedi force would storm his fortress , he had constructed a gigantic network of defensive guns that covered the side of the city facing the open plains , and he reinforced his position with a powerful energy shield . Dassyne was disappointed when he learned that instead of the huge army he had envisioned two Jedi had infiltrated his fortress and deactivated the ray shields . These Jedi were the legendary Generals Obi - Wan Kenobi and Anakin Skywalker , who then attacked with an army small and fast enough to avoid fire from the massive defense batteries of Dassyne ' s fortress . With the shield down , the base was decimated by orbital strikes and starfighter bombardment . During the ensuing firefight , Dassyne was killed . In the same theatre , troops from Eriadu under Wilhuff Tarkin broke out from the salient and besieged Triton , Sluis Van and Xagobah . Around the same time , Jedi Master Nem Bees led Deviss and K Company to depose an illegal government on Orto . In the Serenno theatre , the Republic defeated the Confederacy at the Battle of New Bornalex and again at Ord Radama , hoping to clear the way to the hyperspace crossroads of Celanon and Dooku ' s homeworld of Serenno . In the New Territories , Plo Koon defeated the Confederacy at the Ywllandr system , clearing the way for Ki - Adi - Mundi ' s forces , including the Galactic Marines , to assault the key InterGalactic Banking Clan stronghold of Mygeeto . The Battle of Mygeeto would last weeks , carrying on to the very end of the war . The Felucia theater . The fiercest fighting of the Outer Rim Sieges came in the Felucia theater , which included the Foundry of the Confederacy . At the Battle of Murkhana , the Republic scored a propaganda victory when it successfully closed down the CIS Shadowfeed . On Bal ' demnic , the Confederacy of Independent Systems discovered traces of cortosis in the sea cliffs and attempted to enslave the Kon ' me and mine the cliffs for the lightsaber resistant substance . The Kon ' me rebelled and started the Battle of Bal ' demnic . Soon enough , a clone regiment led by Sha Koon and Halagad Ventor landed on the planet but were attacked by the natives , and soon the Separatists and Republic were expelled from the system . The Battle of Felucia proved to be one of the most fiercely - contested battles of the Outer Rim Sieges , fought in what a veteran of the 501st Legion described as horrendous jungle conditions . Commerce Guild President Shu Mai returned to her headquarters on the planet to make arrangements concerning the liquidation of her holdings . However , the newly Knighted Barriss Offee and the Selonian Padawan Zonder went to Felucia and attempted to capture her , although they were captured . Later , Aayla Secura and Clone Commander CC - 5052 came to the rescue . Unfortunately for them , Shu Mai unleashed a deadly bioweapon into Felucia ' s water systems before escaping . On Saleucami , the fallen Jedi Sora Bulq established a Separatist base . He hired elite Anzati assassins to train the Confederacy ' s own clone army , which was grown from the genetic material of Nikto Morgukai warriors . In response , Quinlan Vos and Oppo Rancisis led a huge Republic force that consisted of A ' Sharad Hett , K ' Kruhk , Sian Jeisel , Aayla Secura , and others , to lay siege to Saleucami , thus beginning the Siege of Saleucami . To prevent a relief of Saleucami , Obi - Wan Kenobi , Anakin Skywalker , Mace Windu , A ' Sharad Hett , Adi Gallia , and several other Jedi agreed to launch a pre - emptive assault on Boz Pity . The " Intervention " dropped out of hyperspace behind the Separatist fleet , but it was caught in the planet ' s gravity and was forced to crash - land on the surface . With the element of surprise on their side , the Jedi and their clone troopers were able to quickly secure the surface installations . In space , the rest of the Republic fleet arrived shortly and engaged in a fierce battle with the Confederacy ships . Meanwhile , the Jedi attacked the Confederacy headquarters , where Dooku , Grievous , and Ventress were waiting . Soon Bayts was killed by Grievous . Later on , Jedi Master Adi Gallia was also murdered by Grievous , held by the neck by Grievous ' s hand while he gutted her with a lightsaber . Kenobi confronted Ventress , managing to redeem her at the last moment , but Dooku and Grievous escaped . Ventress , trying to reach Dooku , was blasted down by a MagnaGuard , which was reacting upon orders from Dooku , who did not want Ventress to delay his escape . Critically injured , Ventress warned Kenobi about the upcoming attack on Coruscant , and apparently died . She later was revealed to be alive , thanks to her healing techniques , as she hijacked a shuttle and took off into parts unknown . Hunt for the Confederate leadership . In an attempt to precipitate the end of the war , the Jedi began actively hunting for the Separatist leadership , including Count Dooku , General Grievous , and the Council of Separatists . Many of the Confederacy ' s top commanders were killed or captured during the course of the Outer Rim Sieges , such as the bounty hunter Durge , who met his end thanks to Anakin Skywalker during the latter ' s mission to Maramere , when his escape pod was driven into a star . On a temporary leave from the battlefront , Obi - Wan Kenobi took on a personal mission to find and neutralize the Dark Jedi Asajj Ventress , whom he believed was still alive and dangerous . With the help of Skywalker , Kenobi followed the trail to Boz Pity , a major Confederacy base surrounded by a fleet of over a hundred warships . By chance , the two Jedi were found by Bail Organa , who was investigating the situation in the Outer Rim . Kenobi then called in a full Republic assault force to lay siege to Boz Pity . On different occasions , Wat Tambor , Nute Gunray , and Shu Mai were all nearly captured when they fled to their respective personal strongholds on Xagobah , Cato Neimoidia , and Felucia . Eventually , General Grievous decided to take the entire Council under his personal protection . Other theatres . Republic forces deployed from Rothana and Excarga sought to clear the outer Corellian Run of Separatists in the Siskeen theatre , engaging at Ryloth . In the Trans - Hydian , a Republic task force spearheaded by the " Praetor " - class battlecruiser " Quaestor " attacked the Separatist shipbuilding world of Pammant in Mon Calamari Space . Aiming to destroy Pammant Docks , tragedy struck when a hyperdrive mishap caused the " Quaestor " to collide with Pammant , fracturing the planet to the core and irradiating the atmosphere . Hundreds of other engagements throughout the Rim locked up millions of Separatist warships in battles with the Republic navy , which was now unable to break off its attack , should the Confederacy once again gain the advantage . The Jedi Generals were spread thinly throughout the galaxy , and they had only their clone soldiers to accompany them . The Republic ' s heartland was now vulnerable to an attack by General Grievous ' personal battle fleet , which was exactly what the Sith wanted : the Yag ' Dhul theatre was abruptly all - but abandoned by the Confederacy to supply warships for General Grievous ' strike at Coruscant itself . Massing at Abregado - rae , thousands of Confederate warships prepared for a jump through the Deep Core to make a final desperation strike at the Republic ' s capital . Victory in the Core . Defeating the Neimoidians . As well as the Separatist territories in the Outer Rim , the Republic also attacked what few Confederate enclaves remained in the Core Worlds . The Trade Federation homeworld of Neimoidia was besieged , as well as the Neimoidian purse world s of Deko Neimoidia , Koru Neimoidia , and Cato Neimoidia . During an assault on Koru Neimoidia , Republic walkers and Juggernauts were unleashed on the Confederate forces . Neimoidia itself was ravaged and the destruction of many Neimoidian grub - hatcheries would catastrophically affect the long - term survival of the Neimoidian species . It was during the Battle of Cato Neimoidia , however , that Darth Sidious ' carefully - plotted schemes almost came undone . The battle was an attempt by the Republic to capture Nute Gunray , Viceroy of the Trade Federation and a prominent member of the Separatist Council . Though the Republic was driving the Confederacy out of the Core and the Colonies , Nute Gunray first went to Cato Neimoidia hoping to escape with as much wealth as he could . Republic Intelligence received information as to his whereabouts , and an army led by Obi - Wan Kenobi , Anakin Skywalker and Jan Dodonna was sent to wait in ambush . However , Nute Gunray managed to escape . Despite this , Cato Neimoidia had been conquered and in the confusion , Gunray had left behind his mechno - chair . This specially built piece of furniture contained a holoprojector that broadcast on an encrypted channel , allowing the Viceroy to communicate directly with Darth Sidious . The Jedi Council then tasked Obi - Wan and Anakin with the mission to follow the trail left by this evidence and discover the identity of Darth Sidious once and for all . Their search took them across the galaxy in an ever expanding search for the Sith Lord . During their search for Dooku , Obi - Wan and Anakin took a detour and sieged a shielded Separatist outpost on a rainy planet . Before departing the planet , they were ordered by Chancellor Palpatine and Mace Windu to conduct a mission to the remote planet of Nelvaan , based on intel that Grievous was hiding there . There , Anakin slew a huge monster and gained the admiration of the native Nelvaanians while interrupting an adolescent ' s rite of passage . They saw his arrival as the sign of a champion known as " Holt Kazed " ( " Ghost Hand " in Nelvaanian , referring to Anakin ' s mechanical forearm ) , who would deliver their land from a mysterious evil . Having endured a painful ceremony , Anakin embarked on a quest to confront the evil . He entered a cave where he received a vision that he would become Darth Vader . Then , he discovered a Techno Union facility that experimented on native captives , turning them into fearsome mutants . He destroyed the facility , though he also touched the minds of the captives and returned them to their families . There would be celebrations in the Nelvaanian village . Four days later , Obi - Wan and Anakin were sent to Tythe with Red Squadron , where Count Dooku was assumed to be hiding . In the ensuing Battle of Tythe , the squadron was wiped out by orbital defenses , leaving Kenobi and Skywalker to enter the LiMerge Power facility alone . There , Dooku set battle droid forces upon them , but Anakin , in a display of raw Force power , brought the ceiling down upon them , the droids and Dooku . The Sith Lord managed to clamber free of the wreckage , and took his solar sailer off - planet to rendezvous with Grievous over Coruscant . The Jedi also escaped the ruins of the chamber , and returned to their flagship . The hunt for Darth Sidious . By this point in the war , it became important for the Jedi to find the Sith Lord supposedly in control of the Galactic Senate . This was done in the hopes of convincing Chancellor Palpatine to relinquish the emergency powers granted to him at the start of the war . The Jedi High Council saw Palpatine as becoming increasingly dictatorial as he accrued more powers , which far exceeded the original provisions of the Emergency Powers Act : the Reflex Amendment and the Sector Governance Decree had effectively allowed him to run the Republic as he saw fit . Mace Windu began to speculate that a figure within the Chancellor ' s inner circle might be the Sith Lord , though the Jedi were as yet unaware that Sidious and Palpatine were the same person . After the various attempts to capture the Separatist leaders , General Grievous collected the Separatist Council and attempted to find a new hideout for them . His first choice was the industrial world of Belderone , but having intercepted the transmission through Gunray ' s captured mechno - chair , a Republic task force under Kenobi and Skywalker lay in wait . In the ensuing Battle of Belderone , Skywalker flew through a wave of turbolaser fire to attack the bridge of Grievous ' s flagship , the " Invisible Hand " . The Confederate ships escaped , however , by opening fire on a refugee convoy , destroying several ships to cover their retreat . The Separatist Council was quickly relocated to Utapau , and then to Mustafar . By ambushing Grievous at Belderone , the Republic had lost the intelligence advantage of the mechno - chair , but by reverse - engineering the device , Republic Intelligence learned of its origin . They soon discovered that Darth Sidious had been operating from an abandoned building in the heart of the Works , on the galactic capital of Coruscant itself . A search team was quickly assembled , and with his disguise quickly unraveling , Darth Sidious played his final card : the Battle of Coruscant . As Supreme Chancellor Palpatine , he delivered a speech that named Mygeeto , Felucia and Saleucami as a " Triad of Evil , " sending half of Coruscant ' s home defense fleet to bolster the Outer Rim Sieges and pacify the planets . Simultaneously he ordered Count Dooku and General Grievous to attack the weakened galactic capital through the use of secret hyperspace routes through the Deep Core . The Battle of Coruscant . At Coruscant , the Separatist fleet under Dooku and Grievous launched a week - long siege of the galactic capital . Confederacy C - 9979 landing craft were unleashed on the capital along with swarms of Vulture droids and Droid tri - fighters . Hundreds of millions of battle droids and tank droids ravaged the streets of Galactic City , causing much damage to lives and property . In response , the Republic deployed its Clone forces against the Separatist droid forces . As the battle raged in space , in the sky and on the ground , Grievous broke into 500 Republica and kidnapped Palpatine , slaying several troops and Jedi in the process . Realizing that they had been lured away from Coruscant , Skywalker and Kenobi made their way back to the capital world with the Open Circle Fleet to join in the attempt to rescue Palpatine . Boarding the Separatist flagship " Invisible Hand " , they made their way through the ship to where the Chancellor was being held . However , before they could escape they were met by Count Dooku , who once again faced off against the Jedi . Although Dooku originally had the upper hand , the Jedi changed lightsaber styles during the middle of the battle in order to put the Sith Lord on the back foot . Dooku quickly swung the battle back in his favor by throwing Kenobi against the wall through the Force and knocking him unconscious . Dooku and Skywalker fought on , with both Dooku and Palpatine urging Skywalker to give in to the dark side . This backfired on Dooku , as Skywalker gained the upper hand , disarmed his opponent . On Palpatine ' s instructions , decapitated Dooku , destabilising the Separatist leadership into the military faction led by General Grievous and the civilian faction led by Nute Gunray . Skywalker , Kenobi and Palpatine were later recaptured by General Grievous , but with the help of R2 - D2 they gained control of the ship and landed what remained of it down on Coruscant . However , Grievous escaped and together with the remains of the Separatist fleet fled to the Outer Rim Territories . The end of the war . The Battle of Utapau . As the Separatists were driven off Coruscant and the Outer Rim Sieges resumed , the end of the war was in sight , but Palpatine stressed that the Separatist threat would not end until General Grievous was destroyed . Clone Intelligence located the Separatist stronghold on Utapau and the Jedi Council assigned Kenobi the task of bringing the General to justice . Arriving on Utapau , he was greeted by Tion Medon , who informed him of the General ' s location . After selecting the services of a varactyl named Boga , Kenobi made his way to the tenth level of Pau City , where he engaged in a brief duel with the General . Not long after , the 212th Attack Battalion , led by Commander CC - 2224 arrived and engaged what little remained of the Separatist droid army . Taking the opportunity to leave , Grievous boarded a Tsmeu - 6 personal wheel bike and fled the scene . Kenobi pursued the General throughout the battle until they reached the General ' s personal Belbullab - 22 starfighter , where they fought once more . Grievous appeared to have the upper hand on Kenobi until the Jedi Master called Grievous ' s blaster to him using the Force . Then he shot him several times , destroying his organs . General Grievous , one of the greatest threats to the Republic in its history , was dead at last . The clones then proceeded to destroy the Anti - Air Turrets so that LAAT reinforcements could be brought in . Republic forces continued to push back the droid forces until they received Order 66 . The Battle of Kashyyyk . On Kashyyyk , a combined Republic / Wookiee force repelled a second Separatist invasion . Kashyyyk was a major navigation hub for the eastern quadrant of the galaxy , making it a strategically important system which had long been a target for the Separatist military . Confederate leaders requested the Wookiees join their rebellion , but the Kashyyyk royal families proved indecisive . General Grievous , having become impatient regarding their decision to join the Confederacy , decided to send battle droids to " persuade " them . The droids unintentionally killed Prince Rikummee , and King Grakchawwaa decided to oppose the Separatists . After a number of probing attacks throughout the war the Separatists finally decided on a full scale invasion of the city of Kachirho in the Wawaatt Archipelago . This was to serve as a literal beach head into the rest of the forest covered planet . To this end the Separatists made particular use of the age old enmity between the native Wookiee and their system neighbors the Trandoshans to prepare for their attack . The Trandoshans did this in a number of ways , in particular by raiding the city and taking its leader , General Tarfful prisoner , using their slaving activities as a cover for the true objective . In secret the Separatists landed a large droid force and prepared for their attack . However , while the system was an important strategic location and both sides believe the battle to be straightforward , it was in fact little more than a diversion by Darth Sidious . The clone commandos of Delta Squad were dispatched to find Tarfful and unite the Wookiees against the Separatists . After rescuing a Wookiee Chieftain , the commandos aided the Wookiee resistance in Kachirho against the Separatist forces , destroying a Commerce Guild destroyer in orbit . RC - 1207 was lost while fighting , and Delta Squad pulled out on a gunship as the Separatist counterattack came . During the aftermath , they discovered they were an advance group for a Republic invasion force . Kashyyyk was considered too important to lose to the Separatists , so battalions of clone troopers from the 41st Elite Corps supplemented by units assigned to the 501st Legion were dispatched to the Wookiee homeworld to aid the Wookiee forces engaged in battle with a Separatist droid army . Yoda held good relations with the Wookiees , and thus became the commanding officer for the Republic forces sent to the system . He was assisted in the direction of the combined forces by General Tarfful and Chewbacca , heads of the local Wookiee defense force . Jedi Masters Luminara Unduli and Quinlan Vos ( having been reassigned from Boz Pity ) were also present . The Separatists were already blockading the planet by the time Yoda ' s forces arrived . However , General Yoda ' s fleet was able to penetrate the blockade and land on the surface . The space battle continued , cutting the detachment of droids already landed off from the rest of the Separatist Fleet . The droid battalions established their command posts and attacked . On the vehicle front , Wookiee flying catamarans were aided by Juggernauts , AT - AP and AT - RT walkers and other assault vehicles . They faced enormous opposition from Separatist droid tanks , OG - 9 homing spider droids and HMP droid gunships . Despite the best efforts of the combined Wookiee / Republic defense , Kachirho soon became in danger of being overrun by the Separatists . Two things managed to save the Wookiees : the sudden deactivation of the droid army and the transmission of Order 66 . Unfortunately , both of these actions would bring about a disaster that would be far worse for them . Order 66 . During the events of the Clone Wars , Palpatine became a father figure to Anakin Skywalker . The young Jedi felt comfortable discussing events with the Chancellor that he hid from even Kenobi or Amidala . Palpatine used Skywalker ' s growing mistrust of the Jedi Council to his advantage , playing against his insecurities by saying that he could offer him much more than the Council ever could . He also revealed his secret identity as Darth Sidious to Skywalker , knowing that he would go to the Jedi Council and report this . Skywalker did report this information to Mace Windu , who arrived at the Chancellor ' s Office with fellow Jedi Kit Fisto , Saesee Tiin , and Agen Kolar , intent on bringing an end to the Chancellor ' s reign . Within moments , however , Windu was the only one alive facing off against the powerful Sith Lord . Skywalker , against Mace Windu ' s orders , arrived at the Chancellor ' s Office and witnessed Palpatine disarmed and cornered by Windu . Taking advantage of the scene , Palpatine succeeded in seducing Skywalker . As Windu was about to deliver the killing blow , Skywalker severed his lightsaber hand , allowing Palpatine to hurl Windu out the window to his death using Force Lightning . Having committed an act of betrayal against a fellow Jedi , Skywalker knew that his options were limited . Pledging himself to Palpatine , he became a Sith and was given the name Darth Vader . His first task was to lead the 501st Legion to the Jedi Temple and eliminate every single Jedi inside . He was then ordered to go to Mustafar to eliminate the Separatist Council . The Great Jedi Purge had begun . Clone troopers of the 501st Legion were transported to Coruscant in several " Venator " - class Star Destroyers that stayed over the city throughout the operation . Marching silently to the gates of the Temple with the clones , Vader commenced , the destruction of the Jedi Temple and all within it , Masters , Padawans and Younglings alike . As Operation : Knightfall was nearing its conclusion , Senator Bail Organa arrived to investigate and witnessed the execution of Padawan Zett Jukassa . The clones who executed Jukassa prepared to fire on Organa , but Clone Sergeant Fox ordered them to stand down , feeling that enough had been killed that night . Fox politely told Organa it was time for him to leave . Organa left , but decided to warn any surviving Jedi of what happened . As Vader eliminated the Jedi at the Temple on Coruscant , Palpatine sent a message to the Clone Commanders stationed across the galaxy , telling them to execute Order 66 . With this transmission , the clone troopers immediately turned against their Jedi commanders . On Utapau , troopers under the command of Cody opened fire on Kenobi and Boga . With the clones assuming Kenobi dead , the fight went on as normal until the battle droids were shut down . On Kashyyyk , Yoda sensed a grave disturbance in the Force as the battle was winding down . This was Order 66 , which was being carried out throughout the galaxy . Clone Commander CC - 1004 received a comlink - call on a frequency - locked channel reserved for the commanders . The image of Supreme Chancellor Palpatine instructed him to carry out the order to kill the Jedi Master , General Yoda . As the clones prepared to execute him , Yoda drew his lightsaber and in one fell swoop decapitated his would - be assassins . Yoda then proceeded to escape into the nearby jungle along with Wookiee warriors Tarfful and Chewbacca . Jedi that were killed during Order 66 included such well known Jedi Masters as Aayla Secura on Felucia , Stass Allie on Saleucami , Ki - Adi Mundi on Mygeeto , Plo Koon on Cato Neimoidia , and Cin Drallig , along with hundreds of other Jedi of all ranks around the galaxy . Jedi that managed to survive the attack included Obi - Wan Kenobi , Yoda , Shaak Ti ( who would be killed by Galen Marek many years later ) , Kazdan Paratus ( who would also be killed by Galen Marek years later ) , Rahm Kota , and A ' Sharad Hett , among a handful of others . The Mission to Mustafar . After his mission to cleanse the Temple of Jedi , Vader took a Eta - 2 " Actis " - class interceptor ( with R2 - D2 in tandem ) to Mustafar . The Separatist Council , having been informed by Sidious . in a deceitful manner , that he would arrive soon , assumed that he was coming to give them a handsome reward . Instead , he viciously slaughtered every single one of them without remorse . Those killed were : Nute Gunray and Rune Haako , with their aide Rute Gunnay , San Hill , Wat Tambor , Poggle the Lesser , Shu Mai and her aide Cat Miin , Passel Argente and his aide Denaria Kee , and Po Nudo and his aide . Nute Gunray was the last to be killed – he begged for peace , but Vader still cut him down . Palpatine then ordered Vader to send a deactivation signal , which was , ironically , originally developed by Geonosian engineer Gizor Dellso ( who would attempt to rebuild the Separatist Droid Army on Mustafar many years later ) to prevent anyone from using the Droid Army against them . Gizor Dellso himself was at one point on Mustafar , but managed to avoid being killed by Vader . The signal was activated and the vast majority of the Confederacy ' s military strength ( which was largely made up of droids ) simply shut down , forcing over 99 % of the Separatist forts and planets to surrender to the Republic , and bringing the Separatist movement to an quick end . With the extermination of their leadership and the prompt - shutdown of most of their forces , the Trade Federation , Techno Union , Commerce Guild , and Corporate Alliance surrendered or dissolved , and their assets were soon subsumed by the Galactic Empire . Aftermath . With both the Separatists and Jedi effectively eliminated , Supreme Chancellor Palpatine spoke before the Senate , declaring an end to the Clone Wars and the reorganization of the Galactic Republic into the first Galactic Empire , appointing himself as Galactic Emperor , ruling with absolute powers for life . He also declared the Jedi to be traitors to the Republic , displaying tampered recordings of his encounter with the Jedi , and that any remaining Jedi would soon be brought to justice . This declaration was met with thunderous applause by much of the Senate , though there were those that held reservations about what they had just heard . Following Palpatine ' s declaration , major changes occurred in the fabric of the former Republic . Members of the Petition of 2000 , delivered to Palpatine in the days prior to the establishment of the Empire , were arrested and charged with treason . The Commission for the Protection of the Republic , formed during the Clone Wars , was merged with the Imperial Security Bureau and renamed the Commission for the Preservation of the New Order . The clone troopers were reorganized under the name Imperial stormtroopers . The war machines of the Republic ( such as the " Acclamator " - class transport and AT - TE ) were retired from active service on the front lines in favor of new weapons of war such as the " Imperial " - class Star Destroyer and AT - AT . The captains of the Republic ships that participated in major conflicts of the Clone Wars ( such as the Siege of Saleucami and recovery of the Rendili " Dreadnaught " - class cruisers ) were given the credit for winning the battles , completely eliminating the Jedis ' involvement . The Clone Wars had ended , the Jedi had been exterminated , the Galactic Republic had fallen , and in its place stood the Galactic Empire . The assets of the Trade Federation , Commerce Guild , Corporate Alliance , Techno Union and InterGalactic Banking Clan were brought under the Empire ' s direct control and administration . With Nute Gunray dead , Acting Viceroy Sentepeth Findos signed a treaty with the Empire at blasterpoint , surrendering control of all Federation assets and dissolving the Trade Federation . This treaty was opposed by Federation customs vizier Marath Vooro , who led a resistance against the Empire until his defeat at the hands of Grand Moff Octavian Grant in the Five Veils Campaign . Though Palpatine declared an end to the Clone Wars with his Inaugural Address , in truth a number of Separatist holdouts remained that the Empire would have to deal with throughout the next decade . Some battle droid forces escaped the deactivation order or were reactivated by Separatist Senators like Toonbuck Toora , who fought on against the Empire . Pockets of Separatist forces collected in the Ciutric sector , the Western Reaches , and the old Foundry of the Confederacy . The majority of these holdouts would be dealt with by 17 BBY with the Imperial Reconquest of the Rim , though the surviving Geonosian engineer Gizor Dellso attempted to continue the Separatist cause possibly as late as 12 BBY . As the last leader of the remaining Separatists , he attempted to churn out a droid army of his own on Mustafar . He was quickly destroyed , however , by the 501st Legion at the Battle of Mustafar , and the last real influence of the Separatists was eliminated . The Clone Wars , as the largest galactic conflict ever during its day , still had consequences that lasted through the ages . It resulted in a distrust of droids by many , in the devastation of many planets , and weakening the galaxy in preparation for Imperial rule . Civilian perception . Galactic Republic . Many civilians in the Republic followed the Clone Wars closely , mainly through the HoloNet and Republic propaganda . Throughout the entire conflict , Republic citizens were overwhelmingly loyal , and dissent was nearly unheard of . This was due in part to simple patriotism but more a product of the pressure to show support . In the tense attitude of the Clone Wars , those who second - guessed the Republic were often looked on with suspicion . Senators , in particular , had to very carefully watch their language , and many fought back accusations of Separatist sympathies when they openly attempted to challenge the questionable ' reforms ' of the Supreme Chancellor . Public sentiment held that Palpatine , in fact , was indispensable as a leader : the Supreme Chancellor conducted himself calmly and projected a sense of steadfast determination in the face of the conflict . He made a show of reluctance at adopting emergency powers , and this and the sense of sorrow he projected at the ongoing conflict led many citizens to trust him implicitly . Therefore , any attempts to rebuke his actions were harshly frowned upon by the majority , as there was a significant fear that without Palpatine leading the Republic , it would have no chance against the Confederacy . Although relatively new to the scene , the clone troopers quickly established themselves as the essential backbone of the Galactic Republic . It was almost immediately apparent , even to the Jedi Council that the limited number of Jedi and no amount of civilian soldiers could provide the kind of military support that the clones could . Bred for the sole purpose to fight and die for the Republic , many throughout the galaxy believed that the clones were just like their battle droid counterparts : " empty " and unfeeling creations with no mind or free will . But as millions of clones continued to lay down their lives for the citizens they had sworn to protect and the Jedi they followed with faith and awe , public sentiment for the clones grew , and many liberal reforms were introduced so that the clones could be treated like men and not expendable machines . At the height of the Clone Wars , the Clone Army of the legendary Jango Fett proved time and again that although they were an " army of one man , it was the right man for the job " . The people loyal to the Republic saw them as a symbol of hope , the Jedi cared for them and saw them as comrades - in - arms , and the clones themselves began to believe their closely - guarded suspicion that maybe they were indeed sentient beings and not just mere products . Personifying the nobility of the Republic cause were the Jedi Knights . The Jedi were larger - than - life heroes whose impossible feats garnered the awe of beings across Republic space . At the forefront of the public eye were the dynamic Jedi duo Obi - Wan Kenobi and Anakin Skywalker , who often worked together to direct campaigns . These two , referred to ubiquitously with the catchphrase " Kenobi and Skywalker " , became the poster boys of the Republic war effort . Throughout the war , sensationalist HoloNet reports lauded and exaggerated their achievements . Wherever the pair went , the Republic inevitably won the battle , or so the HoloNet claimed . These two were especially popular with younglings , who followed their exploits as if they were following the records of athletes . On the other hand , General Grievous was the symbol of the enemy . Along with the adventures of Kenobi and Skywalker , news reports related the atrocities committed at the hands of the cyborg general . Conversely to the famous Jedi pair , wherever Grievous went , the Republic forces were sure to be defeated , sowing fear across the Republic and making more citizens put their faith in the Chancellor . They believed the General to be unstoppable . Indeed , he nearly was . Although optimism was high at the beginning of the war , as it dragged on , morale began to fall sharply . Even the propaganda - laced HoloNet news reports didn ' t manage to stem the growing tide of uneasiness over the odds of a Republic victory . The Grand Army ' s efforts to hold off Grievous were failing . System after system fell to the onslaught of the droid armies , and many planets continued to defect to the Confederacy . Not only that , but the people ' s faith in the Jedi began to wane over the course of the war , when more and more Knights were killed in battle . It became clear that the warriors who had once seemed invincible were mere mortals as well . One of the main causes of the dwindling adoration of the Jedi Order , however , was not the mortality of the Jedi but their susceptibility to treason . Though of course no mention of Jedi traitors made it past Republic news censors , civilians nonetheless learned about the defection of Knights like Sora Bulq , Depa Billaba , Quinlan Vos , and Pong Krell , who had betrayed not only their Order but the Republic itself . Even the leader of the enemy , Count Dooku , had himself once been a Jedi . It was not unexpected , therefore , when the Chancellor ' s Office announced that the Clone Army had turned back a supposed coordinated coup of the Republic by the Jedi Order . Instantly , public sentiment reversed , and with the combined motivation of victory against the Separatists and protection against the supposedly fanatical Jedi , Palpatine was unanimously lauded for his direction of the Republic . His ascension to autocrat was not only unquestioned , it was encouraged . It would only be years later that the people would realize the consequences of their shortsightedness . Confederacy of Independent Systems . Unlike the people of the Republic , those inhabiting worlds that seceded from the government were often less driven by allegiance to the Confederacy than simply by their yearning to transcend their current condition . There were numerous reasons planets seceded . Some were simply unhappy with the way the Republic and the Senate were being administrated . Others were worlds suffering from the aftermath of wars , famines , or other disasters that had been neglected by the Republic . Still others were worlds where tensions or open wars between sects continued to flare . The Confederacy took advantage of these small conflicts , offering assistance to a sect ' s minor war if that faction would contribute in turn to the larger galactic conflict . Count Dooku , a highly adept speaker , made simple , powerful appeals to people ' s spiritual wants and desires for freedom , which won him a reputation as something of a savior and earned him the awed nickname " Gentle Hand " . The Kaleesh of Kalee , the Ishi Tib of Tibrin , and the Balawai of Haruun Kal were three examples of this Confederate policy of outsourcing war . The people of these planets regarded the Separatists as saviors - they had agreed to intervene and decide millennia - long sectional disputes , conflicts the Republic had long refused to take sides in . For the civilians of worlds where the Confederacy had offered assistance , loyalty to their species translated into patriotism for the Confederacy . The defining attribute of nearly all loyal Confederate citizens was hatred of the Jedi . As the leaders of the Republic armies and its deadliest soldiers , the Jedi represented the greatest threat to the new prosperity the Confederacy sought . Many Confederate civilians poured into the image of the Jedi their hatred over the decayed Republic and fear over the atmosphere of uncertainty surrounding the war . Confederate news broadcasts played up the killings committed by Jedi Knights , and were quick to contrast their self - applied title as guardians of peace and justice with their new roles as juggernauts of death that killed those who were simply defending their homes from invaders . The fear in the hearts of many people on Separatist worlds that their homes would be next contributed to an active hatred of the hypocrisy the Jedi Order of the Clone Wars represented . After the Clone Wars , many Confederates would become part of the Rebel Alliance , another reform - minded organization with goals similar to those of the Confederacy , albeit sans the ulterior motive of a Sith puppeteer and ultimately driven by the desire to restore the Galactic Republic rather than leaving it . Behind the scenes . The Clone Wars was first mentioned in " " by Obi - Wan Kenobi and later Princess Leia Organa , although at the time no mention was made about what they actually were . Phrases such as ' during the Clone Wars ' were often mentioned in works to give some evidence of depth in narration . Another early concept for the Clone Wars was a war between the Republic and the Mandalorians as mentioned in " The Galactic Empire Scrapbook " , though this was published less than a year before the script to " " was written . It was widely assumed that the Clone Wars ended long before the establishment of the Empire ; " A Guide to the Star Wars Universe " listed the end of the Clone Wars as 35 BBY ( which was later retcon ned into being the Great ReSynchronization ) , and Mon Mothma in " The Farlander Papers " spoke of the " decades of peace " between the end of the Clone Wars and the rise of the Empire , with Palpatine being elected President during the war but not declaring himself Emperor and exterminating the Jedi until much later . However , in Marvel " Star Wars " comics , the Clone Wars were said to be at a time late enough that Leia Organa was a notable figure , a grown - up Boba Fett fought in the conflict , and " The Emperor " was already in power ; these errors would be collectively retconned by having Leia be mistaken for her mother , Darth Sidious later becoming the Emperor , and " Boba " actually being a rogue clone who was rumored to be the offspring of Jango Fett . During the Bantam era of the Expanded Universe , authors were limited in how they could describe the events of the conflict . Prior to the release of Episode II , the general consensus among fans was that the " Clone " in " the Clone Wars " referred to clones being the antagonists in a war against the Republic and the Jedi , and most Expanded Universe material written prior to 2002 seemed to support this belief . This changed in 2002 , when would tell the events that occurred during this time . Since the release of " Clones " and " Sith " , the Expanded Universe material set in the Rebellion era and the New Republic era or later in the timeline , has made an effort to include the newly revealed information . Such examples can be seen in the " " comic series ( where both " Acclamator " - class warships and AT - TEs can be seen ) , the appearance of an unmasked Boba Fett in several comics and R2 - D2 recounting events from " Revenge of the Sith " ( including and the birth of Luke and Leia at Polis Massa ) , during the " Dark Nest Trilogy " . From 2002 to 2007 , the Clone Wars era was one of the most completely and coherently documented in the Expanded Universe . While there was no date given for some events such as clone troopers adopting Phase II clone trooper armor , most major events of the war were given a specific month on the 36 - month timeline of the Clone Wars , such as Anakin Skywalker ' s knighting ceremony , which took place 30 months into the war . However , the 2008 " The Clone Wars " multimedia project retcon ned the entire timeline to make room for the new continuity , which would not have fit anywhere on the timeline otherwise . Changes include Anakin Skywalker having been knighted shortly after the Battle of Geonosis and the addition of his Padawan , Ahsoka Tano . A definitive timeline has yet to be released .