Clone Wars

right|200px|thumb|From its beginning, the war took its toll on all Jedi...
right|200px|thumb|...as a monastic order turned into an order of warriors...
right|200px|thumb|...to fight a war they were never meant to win...
thumb|200px|right|...because it was never a war in the first place, just a plot.
The Clone Wars (22 BBY–19 BBY) was the name given to the major galactic conflict fought between the Galactic Republic and the Confederacy of Independent Systems. It was thought to be named after the clone troopers used by the Galactic Republic.
Unknown to the bulk of those involved, it was started, maintained and ultimately ended by the Sith Lord Darth Sidious, whose ultimate goal was the transformation of the Republic into the Galactic Empire with him as Emperor as well as the virtual eradication of the Jedi Order.
==Origins== 
 
Although the Clone Wars officially began on 22 BBY at the Battle of Geonosis, their origins can be found ten years prior, during the blockade of Naboo by the Trade Federation. The aftermath saw the election of Naboo Senator Palpatine to the office of Supreme Chancellor of the Republic. He promised to bring an end to the corruption that had so often plagued the Senate. The first few years of his tenure saw very little 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 due to his role in the Naboo conflict (despite opposition from Padmé Amidala.) 
 
During this time, Palpatine (in his alter ego as Darth Sidious) had contacted Count Dooku. Having lost 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, seemed the perfect one to mold. Having killed Sifo-Dyas to seal his fate and become Darth Tyranus, Palpatine ordered Dooku to eliminate any reference to Kamino from the Jedi Archives, preventing the Jedi from discovering the clone army secretly being grown for them until they were ready to learn about it and selected Jango Fett 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. Clonemasters 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 Old 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, declaring his intentions to form the Confederacy of Independent Systems, a group of disenfranchised organizations and governments whose goal was to secede from the Republic. Fearing what would happen if this breakaway faction was allowed to do so, Palpatine was allowed to stay in office longer than the Galactic Constitution permitted.
Over the next two years, many systems left the Republic to join the Confederacy, Ando, Geonosis, Tynna, Sy Myrth and Yag'Dhul among them. They would be joined by the Elrood, Danjar, Tantra and Sluis sectors, bringing the entire Rimward leg of the Rimma Trade Route under the control of the Confederacy. These sectors would be followed by the Abrion Sector which provided the Confederacy with some 200 agricultural worlds and the Lahara Sector which brought over Agamar, Oorn Tchis and the Mirgoshir hyperspace crossroads. However, though Ando joined the Confederacy, the Andoan Free Colonies remained loyal to the Republic.
Over time, they 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 the Trade Federation. Coruscant also found itself the target of many terrorist attacks, including an attack on Naboo Senator Amidala upon her return to vote on the Military Creation Act, which would give the Chancellor the right to create an army to defend the Republic against the Separatist threat. 
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 men with a million already in production. He also met Jango Fett, who attempted to escape to Geonosis, but was followed by Kenobi. Obi-Wan managed to send a message to the Jedi Council, but was captured. On Tatooine, Anakin was ordered by Mace Windu to stay where he was and protect Padmé. Padmé, however, decided to travel to Geonosis to rescue Obi-Wan. However, they were captured as well, and all three were sentenced to be executed.
With the knowledge of the Separatist Army, the Senate, at behest of Senator 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
==The Battle of Geonosis== 
 
Obi-Wan, Anakin and Padmé managed to free themselves, but found themselves trapped once again. However, before they could be killed, Mace Windu arrived with 200 other Jedi. The Jedi were immediately attacked by a massive droid army. Although the Jedi managed to hold their own for some time, their numbers dropped considerably and were being beaten back by the superior 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, seeing the battle lost, took the plans for the Separatist's Ultimate Weapon (the Death Star plans) and fled to a secret hangar. Intercepted by Obi-Wan and Anakin, he managed to best them both, even severing Anakin'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 Palpatine 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.
==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 Side Adepts. These individuals included Asajj Ventress, Sev'rance Tann, Sora Bulq, Tol Skorr, Kadrian Sey, Artel Darc, Karoc, Vinoc, Saato, Trenox, and even the 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 ally recruited to the Confederacy 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 IGBC 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 Army.
==Year one (22 BBY-21 BBY)== 
===Early campaigns===
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 troopers 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 since the Battle of Ruusan a thousand years prior. 
Following the battle, Jedi Knights Sora Bulq and Tholme were sent to Dooku’s hidden base on Bakura to confront him. Unfortunately for them, Dooku captured and seduced Sora Bulq to the dark side though Tholme managed to escape. Seven days after the Battle of Geonosis, Mace Windu sent two Jedi spies (Aayla Secura and Ylenic It'kla) on a mission to Corellia to find the Techno Union scientist Ratri Tane, who possessed very valuable information. Unexpected help came from the Corellian Jedi Master Nejaa Halcyon, having just returned from a failed mission to halt the Freedom's Sons' attempts in the Sluis Sector. 
This was followed by a Separatist/Trandoshan invasion of the Wookiee homeworld of Kashyyyk. There, the Trandoshans rounded up countless Wookiee captives and imprisoned them in concentration camps. Though the Republic managed to drive the Trandoshans off, war would continue to take place on Kashyyyk. 
Following this, the Chiss Commander Sev'rance Tann, led an assault on Tatooine where her agents learned of a new Republic weapon known as the "Decimator" being built on Eredenn Prime. On Eredenn Prime, she captured several Decimators and then captured Alaris Prime, a Wookiee colony world which had just recovered from the Dark Reaper crisis. Tann then made a strike on Sarapin which generated enough geothermal energy to supply a significant amount of the power for the Core Worlds. This created massive blackouts that affected countless Core Worlds including Coruscant. Later on the arctic world of Krant, Jedi General Echuu Shen-Jon slew Sev'rance Tann with his lightsaber after calling on the Dark Side.
===Dark Reaper crisis=== 
200px|left|thumb|Anakin Skywalker and Obi-Wan Kenobi look at the ruins of Kessia following the Battle of Thule
Later, the Republic sent Obi-Wan Kenobi and Anakin Skywalker to Raxus Prime where they discovered Separatist forces on the planet. Millennia earlier, in 3,996 BBY during the Great Sith War, Sith Lord Ulic Qel-Droma had fought on Raxus Prime and unleashed the Dark Reaper on the Republic forces. However, the superweapon was apparently disabled in a mysterious turn of fate 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 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 furthest 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 Dark Reaper and Harvester. 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.
===Defense of Kamino===
This was followed by another Separatist assault on Kamino where Separatist forces under the Corporate Alliance Magister Passel Argente and the Mon Calamari Merai assaulted Kamino 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 flagship the Shark in the process, and 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 cylinders and conscription was introduced throughout the Republic.
===Further campaigns===
300px|left|thumb|Defense of Naboo
Despite losing the Dark Reaper, the Confederacy still continued research on developing weapons. On the Techno Union world of Queyta, researcher Dr. 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, 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 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 Anakin, Obi-Wan and the ARC trooper Alpha 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. 
This victory was later followed by the Battle of Pengalan IV which saw a full platoon of clone troopers sent to Pengalan IV to destroy a diamond boron missiles facility in the city of Tur Lorkin. These missiles were designed to shoot down Republic starfighters. Later, a mission to Qiilura saw Omega Squad being deployed to capture a Separatist research facility on the planet where an anti-clone virus was being manufactured. 
Later, Mace Windu was sent to 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 Coruscant, a group of Korunnai 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. This was followed by the Mission to Queyta, a Jedi mission to obtain an antidote for the chemical weapon known as 'swamp gas', used to wipe out the Gungan colony on Ohma-D'un. Though the mission was successful, the Republic had not seen the last of the deadly swamp gas. Unknown to the Jedi, a second laboratory had 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 .
===Conquest of Muunilinst===
Following that, Palpatine dispatched Anakin and Obi-Wan to lead an assault on Muunilinst. Muunilinst was the headquarters of the InterGalactic Banking Clan which was a heavy monetary and battle droid contributor to the Separatists. During the battle, the Republic unleashed a fleet of Acclamator assault ships on the Separatist defenses. Obi Wan lead the ground assault while Anakin led the space battle. 
On Muunilinst, the Separatist bounty hunter Durge led an assault of IG lancer droids against Kenobi's ground forces. In response, Obi-Wan led a force of Clone lancer troopers on 105-K lancer bikes and defeated Durge's force. He then teamed up with a squad of ARC troopers led by Captain Fordo, who were on a mission in the city of Harnaidan, though their gunship was shot down behind enemy lines. Eventually, Obi-Wan and the ARC troopers raided the InterGalactic Banking Clan's Command Center, and took the Banking Clan leader San Hill into custody, thus defeating the Separatist forces.
Meanwhile in space, Anakin Skywalker was leading the Republic forces above Muunilinst when a mysterious ship engaged him. 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 Obi-Wan. He pursued her to the jungle moon of Yavin IV where they engaged in a lightsaber duel through the jungles and on top of the Massassi temple. In the end, Ventress was defeated, though not killed. Despite this, the Galactic Republic had won a major victory against the Confederacy of Independent Systems.
===Capture of Mon Calamari===
Meanwhile, on the ocean planet Dac, the Mon Calamari Knights under the Jedi Master Kit Fisto defeated the CIS backed Quarren Isolation League. After the battle, Kit Fisto discovered the League was allied with the Moappa, whom Kit discovered were also sapient. Kit informed the Mon Calamari that they needed to make peace with and respect the sapience of the Moappa. Despite this, many members of the predominantly Quarren Free Dac movement fled Mon Calamari, settling on the CIS worlds of Pammant and Minntooine, where the Free Dac Volunteers Engineering Corps created shipyards. Using designs based off Mon Calamari Shipyards blueprints stolen by the CIS 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.
===Battle of Dantooine===
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 B-1 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 leaped towards the seismic tank. Windu cut his way in, disabled the seismic driver, destroyed the tank's droid crew, and knocked out the controls. Leaping clear, Windu watched on as the seismic tank smashed into the ground and exploded. The battle was won for the Republic.
===The defense of Ilum===
At Ilum, Count Dooku sent CIS Chameleon droids to destroy the lightsaber crystal temple on Ilum. At the time of the attack, Jedi Master Luminara Unduli and her newly knighted former Padawan Barriss Offee were in the temple. They defended it valiantly, but the Temple eventually succumbed to heavy damage. The two Jedi were trapped until Master Yoda, who was traveling with Senator Amidala, rescued them. A second skirmish took place on the planet at roughly the same time, with Jedi starfighters and Vulture Droids squaring off above an outpost in the snow.
===The Battle of Hypori===
It was during the Battle of Hypori that one of the greatest threats the Republic would face during this time made his dramatic debut. General Grievous led the droid army on Hypori in the downing of several Republic ships and the deaths of several Jedi, including Tarr Seirr, Daakman Barrek and Sha'a Gi. Only the timely intervention of ARC Captain Fordo and a squad of ARC Troopers prevented the remaining Jedi from being killed as well.
Only Shaak Ti, Ki-Adi Mundi, K'Kruhk and Aayla Secura survived.
==Year two (21 BBY-20 BBY)== 
===Capture of Brentaal IV===
Year Two of the Clone Wars would be a long, hard year for both the Republic and the Confederacy. Following the Battle of Hypori, the Republic received information that a Separatist stronghold on Brentaal IV would be lying dormant for a few weeks opening a window of opportunity. The world of Brentaal IV was a vital link in the Perlemian Trade Route connecting the Core Worlds and the Tion Cluster. Holding this planet would be of great significance to the war effort. 
The Republic sent what should have been an adequate task force for the job, comprising of three Jedi and a strong compliment of clone troops and air land vehicles, with the entire effort being coordinated by Jedi Master Plo Koon, in orbit. However, the information turned out to be false, and the Stronghold was alive, and ready for action. The Separatists' headquarters were controlled by a third-rate Warlord named Shogar Tok, whose personal band of mercenaries was trying to take control of the planet in the name of the Confederacy of Independent Systems.
thumb|right|200px|Shaak Ti fights in the Battle of Brentaal IV
A grand land battle ensued with Republic, and Separatist forces striking, falling back, regrouping, and striking again. Despite this, the stronghold on Brentaal IV was defeated and the Republic scored yet another victory against the Confederacy.
Later, Obi Wan Kenobi and Skywalker destroyed a droid factory at Nivek. The two Jedi would also help retake Terra Sool from the Confederacy. Meanwhile at the Battle of Iktotch, Jedi Masters Mace Windu and Saesee Tiin – himself an Iktotchi defeated the Separatists forces there, thus liberating Iktotch. On Nadiem, a droid army commanded by General Grievous was marching close to a city being evacuated by Jedi Luminara Unduli and Barriss Offee. The Jedi managed to herd the droids into a canyon, and above, they set off explosives, tumbling the canyon walls on top of the droids.
===Haruun Kal Crisis===
This was followed by a campaign on Haruun Kal. Despite the planet not being much of a military target, the system itself was an important jump-point to several Confederacy-held systems that were. Jedi Master Depa Billaba was sent to train the people of the world to fight against the Separatist loyal colonists. The civil war on the planet had been fought for several years but now it was in the Republic's interest to help them. This was successful for a time, but after a voice recording made by Depa Billaba hinted at madness and darkness, Mace Windu was sent to capture his former apprentice. Eventually, after a fight with the dark Korunnai leader, Kar Vastor, Mace put his former apprentice under arrest, and called the Republic cruiser Halleck. 
At this time, the colonists had used the energy signature of Mace's lightsaber to track him to the Korunnai base. The Halleck arrived in-system, and deployed the transport Mace had requested and was immediately attacked by Vulture Droids that had been hidden insystem as part of a clever Confederacy ruse. The transport as well as the Halleck's four support fighters were destroyed and the cruiser, severely damaged, but Mace ordered the Halleck to deploy all the remaining transports and gunships to the surface immediately. The Halleck then withdrew from the system. 
Meanwhile, the Korunnai were being massacred by the attacking militia forces. Mace devised a plan involving a large native lizard, an ankkox, Depa, himself, the dark Korunnai Kar Vastor, several of his personal elite force, Nick Rostu, and a female Korunnai named Chalk. He led the small force in a counterattack against the militia, preceded by the induced stampede of several grassers, the local beast of burden. Most of the success is attributed to the surprise of the militia and their unpreparedness. The small force of Korunnai the Jedi managed to then steal two of the several militia gunships headed high into the atmosphere to meet the Republic transports and to aid them. The two captured gunships attacked the Vulture Droids. The droids programming now logged the transports in the 'no-threat' category and switched the militia gunships to 'enemy' as well as 'priority targets'. Mace's gunships went to ground and began to prepare their next move now that their reinforcements had been greatly depleted. Far above them, the Vulture droids had begun to attack the gunships and decimated them until they were finally called off by the local Confederate authority, Lorz Geptun.
Mace then launched an attack in the night on the comms center in the colonist city, Pelek Baw. His gunships had remained concealed in the steam kicked up from a nearby waterfall and the attack was a complete success. Upon reaching the center, Mace had hoped to call the Republic for more help in the event that the Halleck had been destroyed. He soon discovered that interplanetary communications required a passcode held by Geptun. Mace put his clones in charge of the center and planned to hunt down Geptun. He had ordered the commander of the clones, CC-8/349, to man all the nearby spacecraft with men and to use them as distractions if need be. Finally, he warned the commander against Vastor, who had desired the destruction of the Balawai (colonists) for revenge of all the Korunnai killed in the Summertime war. Mace left with his new attendant, Nick Rostu, and Chalk. During their flight through the city to find Geptun the clone-manned craft attempted to make orbit, against Mace's orders, but were shot down by patrolling Vulture droids and began to rain down on the city creating a firestorm that ravaged the city. Mace attempted to contact the clone commander but Kar Vastor had obviously killed him and ordered the clone suicide runs himself. Mace finally located Geptun and made an agreement involving the surrender of the city of Pelek Baw to the Republic in exchange for peace. Mace, along with the remaining clone troopers, and Nick, returned to the comm center to send the distress message. Inside the center they found the bodies of all the clones and captured militia members... and Kar Vastor along with his elite. Mace ordered the clones to guard Geptun until he could make it to the console and enter the code. Mace's spirit was crushed when a mind washed Depa Billaba launched a sneak attack on him. He was forced to fight his former Padawan until she finally collapsed, in a coma to the floor. Vastor's elites and the clones all died in the battle that ended when Nick and the last of the elites locked together. Nick shot the elite and killed him but was stabbed in the stomach by one of the elite's vibroshields. Mace, tired and broken, then faced off against Kar Vastor while Geptun sent the message. Mace severed Vastor's hands using a fallen virbroshield and arrested him for trial. Geptun emerged from the small compartment containing the communications console to find Mace the only one remaining on his feet until Mace, too, fell from exhaustion.
Haruun Kal was taken. Depa Billaba never emerged from her, believed self-induced, coma, having said numerous times on Haruun Kal that she could not be saved and that she was irredeemable. Nick Rostu was saved but never managed to take part in Mace's offer for him to become an officer of the Republic. Kar Vastor was held in the Jedi Temple to await his, and Depa's charges of Crime against civilization. And so Haruun Kal was taken but at great cost in men, morals, and forever marred the war in Mace's eyes.
===The war drags on===
A Separatist fleet appeared over Balamak, an important food-producing world, and established a blockade. General Obi-Wan Kenobi and Nanda-Ree Jando 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. 
On Devaron, a Jedi task force consisting of Kit Fisto, Aayla Secura, the Dark Woman, Tholme and the Neti T'ra Saa arrived to halt a smuggling operation that Aurra Sing and Senator Vien'sai'Malloc had started. Aurra Sing was captured and imprisoned at the Oovo IV asteroid prison though she managed to escape. On Antar 4, Antarian Separatists backed by Count Dooku overthrew the Jedi-allied Antarian Rangers that enforced law on the moon. It was on Antar 4 that Quinlan Vos succeeded in infiltrating Dooku's cadre of Dark Jedi. 
Meanwhile on Bassadro, Jedi Knight Empatojayos Brand led his battalion of clone troopers to the dormant volcanic ranges that offered cover to the Separatist forces. 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. This battle resulted in the galactic public having two rival propaganda machines to choose from: the Republic nationalized HoloNet and the Confederacy's pirated Shadowfeed. The Separatist aligned Corporate Alliance also founded and marketed both anti-Jedi and anti-Republic propaganda which helped keep the public in Confederate territory pro-war. The Hyper-Communications Cartel was also established by the Confederacy to manage its private HoloNet channels and also broadcast Confederacy propaganda and anti-Republic news on its signal.
The propaganda broadcast by both sides polarized many people. For example, in the Republic, the fanatical pro-human COMPOR and the SAGroup were formed. Later on Coruscant, COMPOR pressured Tannon Praji into deporting from the capital all members of species whose homeworld had joined the CIS. 
During an assault on Coruscant, Count Dooku infiltrated the capital world with a small force of Cortosis battle droids and attempted to destroy the Jedi Archives in the Jedi Temple. However, he was driven off by Anakin Skywalker. This battle, coupled with the Sarapin blackout meant Coruscant's citizens no longer felt safe from the war's ravages. Such incidents prompted the Republic to implement numerous changes on Coruscant in the name of increased security. Huge stretches of the cityscape were transformed into military staging areas and clone troopers were seen everywhere. Also on Coruscant, Omega Squad, Delta Squad, a unit of Null ARC troopers and their Jedi Generals Etain Tur-Mukan and Bardan Jusik pursued a Separatist terrorist group along the skylanes and the underworld of the ecumenopolis. 
On Cartao, Palpatine discovered the existence of Spaarti cloning cylinders. A battle with Separatist forces ensued, and most of the cloning cylinders were destroyed. Those that remained were sent in secret by Palpatine to Wayland and Byss. 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 CIS. Diplomacy failed, but the ruling Five Families were killed in a bombardment targeted by A-98. Later, during a mission to the Chykin Cluster, Delta Squad was again assigned to rescue the Acclamator assault ship Prosecutor from Trandoshan mercenaries aligned with the CIS. The commandos liberated the ship and defeated the Trandoshans.
===Battle of Jabiim===
This was followed by the Battle of Jabiim which proved disastrous for the Republic despite defeating Confederacy leader Alto Stratus during the month long battle. 
During the battle, the battlefields of Jabiim were arduous, and combatants would have to contend with the harsh conditions. The Republic could not count on air support due to electrically charged atmospheric disturbances. They instead relied on AT-XT, AT-TE and newly constructed AT-AT walkers as the bulk of their mechanized assault. 
The Jabiim Separatists, however, having lived amidst the rain and mud, were much better suited for combat. Alto Stratus' elite guards, the Nimbus, wore specialized repulsorlift skates that allow them to glide across the molasses-like mud. This gave them a considerable advantage in the combat that followed. Eventually, along with battle droids supplied by Dooku, the Jabiimites were able to destroy the Republic's Shelter Base in the second week of the Battle of Jabiim. It was believed that Obi-Wan Kenobi along with the ARC trooper Alpha perished during the conflict, although they were captured by the Confederacy and shipped to Rattatak. 
His apprentice, Anakin Skywalker, had to lead a group of similarly "orphaned" Padawans in an attack against the Jabiimites. Though Alto Stratus was slain, his fiery rhetoric had leaked to the galactic-spanning HoloNet, and the Confederacy spread his propaganda to many planets, further fomenting secession and rebellion. Despite defeating Confederacy leader Alto Stratus during the month long battle, it ended disastrously for the Republic which lost thousands of Clone troopers and was forced to abandon the Jabiim loyalists to the Confederacy. 
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 was raised and trained on Coruscant itself, rather than the sterile environment of Kamino. These red-emblazoned troops eventually became a familiar sight across Galactic City on Coruscant where they operated as law enforcers, patrolling public plazas and guarding government buildings and landing platforms. These deadly clone troopers were created by Palpatine, the War Council Advisory Panel, and the Homeworld Security Command.
===The Battle of Aargonar===
thumb|right|200px|The Battle of Aargonar
Just days after the Battle of Jabiim, Jedi Knights A'Sharad Hett, Bhat Jul, and Anakin Skywalker were sent to Aargonar to defeat the Separatists there. The planet itself was considered insignificant save for the fact it lay on the border between Republic and Separatist space. The battle fared badly for the Republic with Bhat Jul killed in battle, along with many clone troopers. Ki-Adi Mundi gave the order to retreat, and took a command gunship to ensure he had a full tactical view, whilst Bultar Swan was tasked with destroying the Republic camp to keep the supplies from falling into the hands of the enemy.
Meanwhile, Anakin and Hett, who had gone into a cave to hide, where Anakin accidentally revealed the truth of his slaughter of Tusken Raiders to Hett by mistaking him for a Tusken and almost killing him, found a disabled gunship, and used it to lure a Gouka dragon into the Separatist forces, and give the Republic time to retreat. Hett decided not to tell anybody, but Anakin did not plan to either. Following the battle, the Jedi returned to New Holstice. 
On Parcellus Minor, the Separatists scored a victory against the Republic forces there 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 Republic and Separatist ground forces.
===Escape from Rattatak===
Meanwhile, Obi-Wan Kenobi and the ARC trooper Alpha were imprisoned by Asajj Ventress on Rattatak where she interrogated and tortured them. Despite her efforts, the duo resisted her attempts to crush them. In response, she fed Kenobi muscle maggots that ate away his strength and also placed him in a Sith torture mask to prevent him from manipulating the Force. For Alpha, because of his training and indoctrination, she realized that he would have to be executed soon. However, she underestimated Kenobi and Alpha. For 26 days, Kenobi had exerted what little Force power he could gather to slowly bend the water pipes in his cell. 
Finally, with a final push, the pipes broke and Ventress's dungeons began to flood. With the Sith mask removed by Alpha, Kenobi regained his strength and both proceeded to free the other prisoners, thus creating chaos. He then recovered his lightsaber and that of Ventress’s late mentor. While attempting to escape on a starship, they encountered Asajj Ventress who attempted to stop them from escaping. However, despite his weakened state, Kenobi managed to escape Rattatak. 
Anakin had been assigned to Ki-Adi-Mundi, whom was serving with a Jedi section that was on patrol in hostile space, on the look out for both Separatist and pirate forces. Their job was worsened by the fact that the Senate had recently passed a new Security Act that imposed a mandatory death sentence on pirates. 
Previously, pirates were only had to surrender themselves into the custody of the Republic Navy and the Jedi Order, now they were forced to fight to survive. Thus, when Ki-Adi-Mundi, Anakin, Adi Gallia and Plo Koon encountered a pirate ship near Varonat, a fierce battle ensued. However, it was cut short by the sharp-shooting of Anakin. During the fighting, Anakin was distracted by a warning through Force that told him Obi-Wan was still alive and nearby. 
Meanwhile, Obi-Wan and Alpha had arrived on nearby Riflor. There they faced resistance from Asajj Ventress’s troops and bounty hunters. 
Just as it seemed that their days were numbered, Anakin and Ki-Adi-Mundi arrived and defeated the enemy. They then went to the Republic base where Anakin and Ki-Adi-Mundi were based. Kenobi and the ARC trooper reported back for duty, and Alpha was assigned to Kamino to train a new batch of Clone Commanders. However, the Republic military command, having heard Kenobi’s report on Alpha decided that future Clone Commanders should be designed with more independence and intuition. Meanwhile Kenobi was reunited with his Padawan and would later brief the Jedi Council on what he had discovered about Asajj Ventress.
Throughout the conflict, though many in the Galaxy resented the Jedi, worlds freed from Confederacy control often saw the Jedi as liberators and Anakin found that his star was rising. Following news of his exploits, the Republic media dubbed him "the hero with no fear" and Anakin soon found out that entire worlds under Separatist control expected him to liberate them. On Virujansi, having liberated the world from the Confederacy, Anakin was dubbed by the grateful Virujansi as their "warrior of the infinite". However, the Republic suffered a loss when Togoria voluntarily defected to the Confederacy of Independent Systems.
===Conquest of Duro===
Worse was to come for the Republic when Grievous launched Operation Durge's Lance which saw the Confederacy conquer 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 bombardment 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 issues 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. 
It was also revealed that, in reality, the Committee's chairman, Rodian Senator Onaconda Farr, had reassigned the ships to Iseno after being bribed with contracts for rebuilding on Ando by the Isenese senator, Ronet Coorr. After the release of the report, both Coor and Farr resigned from the Senate. A public backlash against both the Senate and Rodians in general was provoked, with calls for giving the Supreme Chancellor full power to conduct the war and for giving Humans command of fleets stationed around rival planets. A full investigation of Senate Action Subcommittees was launched with the goal of restructuring, and possibly even eliminating them. It is possible that this political restructuring also could have been one of the events that lead to the Sector Governance Decree.
===Victory versus Bulwark===
The ancient shipyards at Foerost in the Deep Core had been churning out warships for millennia. Towards the last centuries of the Republic, the Techno Union 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-class Battlecruiser—a 1,000 meter long warship equipped with powerful weapons and enough armor for ramming smaller vessels. Under the command of the Sullustan Dua Ningo, the Bulwark Fleet smashed through the Republic blockade at Foerost and proceeded to terrorized 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 defeated. Screed and Dodonna would return to Coruscant as heroes for the Republic.
==Year three (20 BBY-19 BBY)==
 
===MedStar===
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 Units or RMSUs and "Rimsoos" on Drongar, a planet of steam fissures and lighting strikes with the most advanced plant life being fungus. 
It was home to Bota, an ugly mold which worked on a wide range of species as an antibiotic, painkiller or even an intoxicant. Having realized its importance and learnt that bota deteriorated quickly when once picked, both sides maintained harvesting operations on Drongar and battles were fought over the Bota fields. It was here that Padawan Barriss Offee arrived to practice her skills as a Jedi healer. She would discover that bota enhanced her Force powers. 
Barriss also met a young surgeon named Dr. Jos Vandar. However, she discovered that Admiral 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 attacked the bota fields. The Republic also tested a superlaser project on Drongar using a modification of the weapons deployed by the SPHA-T walkers. Later, Barriss returned to Coruscant and was promoted to a Jedi Knight while Vandar was reassigned.
===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 Bly attempted to recapture the Scientific Information Packet aboard the Gahenna which had been captured by the native Noghri and kept in an ancient Rakatan 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 for ever.
===Atrocities of Grievous===
Having conquered Duro, Grievous continued his rampage throughout the galaxy. He was responsible for an hour-long orbital bombardment by the Separatist starfleet under his flagship the Invisible Hand which melted the crust of Humbarine, an ancient city world and Core Founder. He would also be responsible for releasing the Loedorvian Brain Plague into the Weemell Sector, killing most of the Sector's Human inhabitants. He personally attacked Alderaan. He also supervised attacks on 26 strategic Loyalist worlds. On Vantos and Nadiem, many civilians and soldiers were murdered. He also collected the lightsabers of fallen Jedi 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. 
This prompted many Jedi to call for the death of General Grievous. 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 Kypo and Tone.
===Republic terrorism===
During the conflict, the Republic had been wrong on several occasions including the devastation of Orleon by Stone mites. Prior to this, the CIS scientist 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 stonemites then ravaged Kishi until Jedi healers proficient in the art of Morichro destroyed them. Armand Isard, director of the Senate Bureau for 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 stonemites 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.
===Victory on Praesitlyn===
Recently, Praesitlyn had been conquered by the Republic. Despite possessing an advanced communications system that linked data feeds throughout the galactic quadrant, the planet had few defenses. Fearing that it would be attacked by the Confederacy, the Republic tried to get a fleet from nearby Sluis Van which possessed shipyards. 
However, Asajj soon discovered their plans and dispatched a fleet under the Banking Clan Admiral Pors Tonith. Having blockaded Sluis Van, Tonith's fleet went to Praesitlyn and conquered it 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.
However, Captain Zozridor Slayke of Freedom's Sons attempted to stop the Separatists though his forces were defeated. Luckily, Republic reinforcements arrived under Nejaa Halycon and Anakin Skywalker. This resulted in the Battle of Praesitlyn which was fought over Praesitlyn and the Intergalactic Communications Center. During the battle, the Republic and the Praesitlyn Defense Force 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.
Later on Susevfi, Nejaa Halycon died during a battle against the Anzati Dark Jedi Nikkos Tyris. However, the Anzati also died during the duel, thus turning his followers the Jensaarai against the Jedi. The Jensaarai would remain isolated from the rest of the Galaxy until discovered many years later by Corran Horn, grandson of Nejaa Halycon.
===Dreadnaughts of Rendili===
The Core World of Rendili, a major starship producer, voluntarily defected to the CIS. Its defense fleet was composed of the then state-of-the-art Dreadnaught-class Heavy Cruisers that could be a valuable asset to the Confederate Navy though 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 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 Yago. Yago hoped to break the Republic blockade with these hostages. However, Saesee Tiin refused to back down. Soon, Obi-Wan Kenobi and the 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 Dreadnaughts to prevent their escape into hyperspace. During the battle, Yago was slain by Jace Dallin. With the end of the battle, the captured Dreadnaughts 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 Obi-Wan 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, Anakin 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, Asajj survived and managed to escape Coruscant.
===Outer Rim Sieges===
By this time in the war, it appeared that the Republic had momentum on its side. It had recaptured key worlds in the Core and the Colonies including Duro, Commenor and Balmorra, driving the Confederate Navy to the Mid Rim and Outer Rim. Thus began the Outer Rim Sieges, which marked the final phase of the conflict.
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. Gruelling engagements began on Ord Radama, Ossus, Ryloth, and elsewhere in an effort to force the Confederacy to surrender.
On Bomis Korri IV, 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 theatre 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.
On Saleucami, the fallen Jedi Sora Bulq established a Separatist base. He hired deadly, elite Anzati assassins to train the Confederacy's own clone army, which was grown form 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, Jeisel, Aayla Secura, and others, to lay siege to Saleucami, thus beginning the Battle of Saleucami.
Oppo Rancisis was later killed by Sora Bulq. Quinlan Vos worked together with Jedi Master Tholme to kill Sora Bulq and Tol Skorr. Quinlan Vos, A'Sharad Hett, Aayla Secura, K'Kruhk, Tholme, and Jeisel all survived that mission. Stass Allie was later assigned to go back there when the planet was taken over by the Separatists yet again.
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 at the hand of Anakin Skywalker during the brief Battle of Maramere. 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, Obi-Wan 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.
Onboard the Star Destroyer Intervention, 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, and was later avenged by Mace Windu. Obi-Wan confronted Ventress, managing to redeem her at the last moment, but Dooku and Grievous. Ventress warned Obi-Wan about the upcoming attack on Coruscant, and died. She later was revealed to be alive, as she hijacked a shuttle and took off into parts unknown.
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. 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.
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. 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.
==Final campaigns (19 BBY)==
 
===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 Republic Senate, and made finding out the identity of the Sith Lord their top priority. This was done in the hopes of convincing Chancellor Palpatine to relinquish the emergency powers granted to him at the start of the war.
Anakin Skywalker, having become the supposed "poster child" of the war (at least in the eyes of everyone), was given the rank of Jedi Knight in part due to his role in the The Praesitlyn Conflict. He was among the Jedi who took part in the Outer Rim Sieges, which included attacks on major Separatist installations on Saleucami, Felucia, Mygeeto, Neimoidia, Cato Neimoidia, Deko Neimoidia and Koru Neimoidia. During an assault on Neimoidia, Republic walkers and juggernauts were unleashed on the Confederacy forces. Neimoidia was ravaged during the battle and the destruction of many Neimoidian grub-hatcheries would affect the Neimoidian species.
It was during the First Battle of Cato Neimoidia that evidence of Darth Sidious finally came into light. 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 went to Cato Neimoidia wishing to take as much wealth with him as he could. Republic Intelligence received information as to his whereabouts, and an army led by Obi-Wan Kenobi, the newly Knighted Anakin and Jan Dodonna was sent to wait in ambush. 
However, Nute Gunray managed to escape. Despite this, Cato Neimoidia had been conquered and Gunray's Mechno-chair had been captured. 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.
Meanwhile, the Commerce Guild President Shu Mai returned to her headquarters on Felucia to make arrangements concerning the liquidation of her holdings. However, the newly Knighted Barriss Offee and Selonian Padawan Zonder went to Felucia and attempted to act against her though they were captured. Later, Aayla Secura and Commander Bly came to the rescue. Unfortunately for them, Shu Mai unleashed a deadly bioweapon into Felucia's water systems before escaping.
Later, Grievous collected the Separatist Council and attempted to find a hideout for them. His first choice was Belderone, though they were forced to flee after it became known to the Republic after a transmission was intercepted by Nute Gunray's mechno-chair. A Republic taskforce under Kenobi and Skywalker lay in wait. During the battle, Skywalker flew through a wave of turbolaser fire and shot at the bridge of Grievous's flagship the Invisible Hand. 
However, the Invisible Hand escaped by opening fire on a refugee convoy. However, by ambushing Grievous at Belderone, the Republic had found out how to decipher the code. By reverse-engineering the device, Republic Intelligence learnt of its origin and soon discovered that Darth Sidious had been operating from an abandoned building in the heart of the Works, on the galactic capital Coruscant itself. By then, Sidious had realized that his disguise would not hold for long. As Supreme Chancellor Palpatine, he delivered a speech that named Mygeeto, Felucia and Saleucami as a "Triad of Evil" and then sent half of Coruscant's fleet to pacify the planets. However, he also ordered Count Dooku and General Grievous to attack Coruscant through the use of secret hyperspace routes that went through the Deep Core.
200px|left|thumb|General Grievous on Coruscant
Meanwhile, Obi-Wan and Anakin went to the remote planet of Nelvaan believing 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 Kezed ("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 then 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. After that, Obi-Wan Kenobi and Anakin Skywalker returned to their Venator-class Star Destroyer and after hearing reports of a Separatist assault on Coruscant, departed back to the capital.
===The Battle of Coruscant===
Meanwhile on Coruscant, the Separatist fleet under Dooku and Grievous launched a week-long siege against the galactic capital. Confederacy C-9979 landing craft were unleashed on the capital along with swarms of Vulture droids and Tri-Droid Fighters. Legions 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 were lured away from Coruscant, Anakin and Obi-Wan made their way back to the capital world to join in the attempt to rescue Palpatine. Boarding the Separatist flagship Invisible Hand, they were met by Count Dooku, who once again faced off against the Jedi. Their battle was vicious, but Anakin secured the upper hand, disarmed his opponent and, at Palpatine’s prodding, killed Dooku.
===The Battle of Utapau===
As the Separatists were driven off Coruscant, 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 Obi-Wan 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 Cody arrived and engaged the Separatist droid army.
Taking the opportunity to leave, Grievous boarded a Tsmeu-6 personal wheel bike and fled the scene. Obi-Wan 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 Obi-Wan until the Jedi Master used Grievous' blaster to ignite his internal organs and bring the General to a messy end. The clones then proceeded to destroy the Anti-Air Turrets so that LAAT reinforcements could be brought in. Republic forces continued to lead a winning battle against the droid forces until Order 66 was called for, in which they opened fire on Obi-Wan and Boga. Presuming Obi-Wan dead, the fight went on as normal until the Battle Droids were shut down.
===The Battle of Kashyyyk===
Meanwhile on Kashyyyk, a combined Republic/Wookiee force repelled a second Separatist invasion. Kashyyyk was considered a major navigation hub for the southeast quadrant of the galaxy, making it a strategically important system which had long been a target for the Separatist military. Confederacy 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.
Later, the clone commandos of Delta Squad were dispatched to find Tarfful and unite the Wookiees against the Separatists. After rescuing Wookiee Chieftain Tarfful from Trandoshans and General Grievous, who had commanded the first part of the battle, the clone commandos of Delta Squad aided the Wookiee resistance in Kachirho against the Separatist forces, destroying the Commerce Guild destroyer in orbit. Sev was captured, and Delta Squad pulled out onto 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) was 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 CIS 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.
Master Yoda sensed a grave disturbance in the Force as Order 66 was carried out throughout the Galaxy. Clone Commander CC-1004, nicknamed Gree, received a comlink-call on a frequency-locked channel reserved for the clone commander. The image of Supreme Chancellor Palpatine instructed him to carry out the embedded order to kill the Jedi Master, General Yoda.
As the clones prepared to execute him, Yoda withdrew 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.
Outside, the battle between Republic and Separatist forces appeared to be over: Wookiees stacked destroyed droids while clone troopers assessed the damage to their equipment and began preparing for a full-scale invasion of Kashyyyk. Jedi Master Luminara Unduli was talking with eight clone officers standing in a circle around her when they executed Order 66. Jedi Master Quinlan Vos was riding on top of a Kuat Drive Yards HAVw A6 Juggernaut; the main cannon of the nearby Juggernaut destroyed the tank, although he was able to survive.
As the Republic forces that came to defend the planet from the invaders became the invaders and executed their commanders in cold blood, the Battle of Kashyyyk was over. The Republic forces soon pulled out of the system, allowing the Wookiees to begin salvaging the masses of wrecked military hardware that the battle had left strewn across the world.
==The seduction of Anakin Skywalker==
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 Obi-Wan or Padmé. Palpatine used Anakin'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 Anakin, knowing that he would go to the Jedi Council and report this.
Anakin 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, and facing off against a powerful Sith Lord. Palpitine allowed Windu to defeat him knowing it would look like an assasination attempt by Mace on a weak old man. Palpitine succeeded in seducing Anakin and as Windu was about to deliver the killing blow Anakin severed his lightsaber hand, allowing Palpitine to hurl him out the window using force lightning. Having committed an act of anger against a fellow Jedi, Anakin knew that his options were limited. Pledging himself to Palpatine, he became a Sith Lord and given the name of 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.
==The end of the Clone Wars==
As Vader eliminated the Jedi at the Temple, 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. 
Jedi that were killed during this attack included such well known Jedi Masters as Aayla Secura, Luminara Unduli, Shaak Ti, Ki-Adi Mundi, Plo Koon, Stass Allie and Cin Drallig, along with Padawans Bene, Whie Malreaux and Zett Jukassa. Jedi that managed to survive Order 66 included Obi-Wan Kenobi, Yoda, A'Sharad Hett, Jeisel, K'Kruhk, and Quinlan Vos.
thumb|200px|right|Darth Vader kills Nute Gunray, bringing an end to the Clone Wars
After his mission to cleanse the Temple, Vader took a Eta-2 Actis-class light interceptor (with R2-D2 in tandem) to Mustafar. The Separatist Council, having been informed that he would arrive soon, assumed that he was coming to protect them. 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 Gizor Dellso 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.
==Aftermath==
With both the Separatists and Jedi defeated, the newly self appointed Emperor Palpatine spoke before the Senate, declaring an end to the Clone Wars and the formation of the Galactic Empire. He also declared the Jedi to be traitors to the Republic, 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 Preservation of the Republic, formed during the Clone Wars, was merged with the Republic Youth Brigade and renamed the Commission for the Preservation of the New Order. The clone troopers were reorganized under the name Imperial stormtroopers. The assets of the Trade Federation, Commerce Guild, Corporate Alliance, Techno Union and Intergalactic Banking Clan were brought under the Empire's control. 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 Jedi's involvement. 
The Clone Wars had ended; the Republic had fallen, and in its place stood the Galactic Empire.
Gizor Dellso, however, survived the Separatists' purge and attempted to continue the Clone Wars as the last leader of the remaining Separatists by churning out his droid army on Mustafar, was quickly blasted down by the 501st Legion, and the last real influence of the CIS was destroyed.