Imperial Civil War The Imperial Civil War was , in fact , not a single war but instead a series of conflicts that plagued the Galactic Empire in the aftermath of the Battle of Endor ( 4 ABY ) and again following the second reign of Palpatine . It officially ended in 12 ABY with the purging of the last major warlords by Admiral Daala . This act resulted in a reunified ( but much weakened ) Empire . New Order purists named it the War of Purification , those who opposed the Imperial Military called it the Imperial Mutiny , and many others labeled it as the Time of Destruction . The death of Emperor Palpatine at the Battle of Endor marked the beginning of the end for his Empire . The Galactic Empire was far too large to be destroyed in one blow , however , and for the next decade or so it was ruled by former Imperials styling themselves as independent warlords as well as loyalists such as Grand Admiral Thrawn and former Director of Imperial Intelligence Ysanne Isard . Empire divided . Immediately following the Imperial defeat at Endor , Grand Vizier Sate Pestage seized control of the Empire . He , however , lacked the charisma , political skill , and , most importantly , the Force , which the late Palpatine and Darth Vader had used to hold the New Order together . Admiral Blitzer Harrsk was the first Imperial to declare himself independent and found his own private fiefdom , and he would not be the last . Later warlords included Admiral Treuten Teradoc , Admiral Zsinj , and General Sander Delvardus , to name the most prominent . Pestage managed to hold the throne for a scant six months before he was deposed by the Imperial Ruling Council . The three Tribunes that made up this group were in fact acting under the influence of Ysanne Isard , and their rule was soon replaced by her . Ysanne Isard succeeded in maintaining the Empire and fending off aggressive warlords for nearly two years . In 5 ABY the Central Committee of Grand Moffs was formed in an attempt to subvert Ysanne ' s rule . Knowing herself to be losing control , Ysanne charged her scientists with breeding a biological virus which targeted only non - humans . In 7 ABY Isard released this virus during the New Republic ' s liberation of Coruscant . Knowing she could not stay on Coruscant any longer she escaped to Thyferra pursued by members of resigned Rogue Squadron and started the Bacta War . At the end of that campaign , Isard was believed to be dead . The remnants of the Empire soon found themselves sharing a common enemy with the New Republic for the first time as both governments viewed the rogue warlord , Zsinj , as their greatest threat . Zsinj came under pressure from both states , but it was not until Admiral Rogriss allied with New Republic General Han Solo that they managed to check him and later kill him at the Battle of Dathomir . The Empire continued to be beaten back until the return of Grand Admiral Thrawn . As the last legitimate Grand Admiral he was able to gather Imperial forces and mount a campaign that reclaimed nearly half of the galaxy for the New Order , despite his non - human identity . This unforeseen resurgence came to an end , however , with Thrawn ' s assassination by his own Noghri bodyguard , Rukh , who had defected to the New Republic . Captain Gilad Pellaeon , Thrawn ' s capable second - in - command , knew his limitations , as well as those of his command , and ordered a retreat . The New Republic immediately took advantage of the Imperial power vacuum and moved to cut off future threats by allying themselves with the remaining warlords . Using the pretext of pursuing Imperial war criminals and other miscreants , the New Republic began their push against Prince - Admiral Delak Krennel . Despite Krennel ' s new ally , a cloned Ysanne Isard , and Isard ' s machinations to steal back her Super Star Destroyer , the " Lusankya " , the New Republic emerged victorious and began pressing their advantage even more . All this left the Core Worlds with only minimal protection . Imperial unrest on Coruscant . In 10 ABY the surviving Imperial warlords , encouraged by what Grand Admiral Thrawn had so recently accomplished with so little and in such a short time , agreed to organize under the Imperial Ruling Council ( secretly with the complicity of the reborn Emperor Palpatine ) for an offensive thrust into the Galactic Core . The New Republic could not match the military might of the re - unified Empire , and after a short , decisive campaign the Empire had retaken the former Imperial Center in the Second Battle of Coruscant . Having taken Coruscant , the Ruling Council decided the time had come to assemble a new Imperial Senate that would serve the Galactic Emperor . The governors , Moffs , and Grand Moffs agreed but with the requirement that they too would be granted seats in the Senate and that their votes would be weighted for the number of worlds they controlled . The Councilors , however , refused as this would in effect decentralize power and share it among local rulers . Matters quickly fell apart . The Imperial military sought to take power itself , but a split between the Army and the Navy occurred . The latter insisted that it alone could choose a new Supreme Commander . Then the bureaucrats and COMPNOR attempted a coup , claiming that any change to the New Order would invalidate the Empire ' s existence . The ISB and Imperial Intelligence , in turn , embarked on a campaign of assassinations against each other . The Dark Side Adepts alone kept out of this inter - factional maneuvering . An armed conflict soon broke out amongst the various Imperial factions on Coruscant , with nearly three Sector Fleets annihilating each other in orbit , and the Split Imperial Army laying waste much of the planet . The chaos then spread across much of the recently - recaptured galaxy , with notable events including the Star Dreadnoughts " Whelm " and " Panthac " destroying each other over Alsakan , the Captain of the " Vengeance " - class dreadnought " Javelin " ramming his ship into a Torpedo Sphere defending Chasin , and squadrons of droid TIEs destroying the " Mandator " III - class dreadnought " Aculeus " at Drearia . The hostilities ended only when the reborn Emperor Palpatine declared his return several months later . However , Palpatine deliberately didn ' t attempt to quell the mutiny sooner out of revenge , personally referring to the carnage as " culling the weak " , and may even have encouraged this internecine conflict through his use of the dark side of the Force . While most of the rank - and - file returned to loyal service , along with some of the warlords , many of the warlords instead chose to flee for their lives as the Emperor was not expected to take kindly to their usurping of his throne . The Imperial Mutiny played into Palpatine ' s plans to establish a " Dark Empire " , a galaxy - spanning government ruled directly by the dark side of the Force rather than military might . Return of Palpatine . By transferring his spirit into a newly cloned body , Palpatine was reborn and rose back to power , after which he proceeded to rebuild the Empire . It only took him 6 years to regain the strength necessary to challenge the New Republic . Having regrouped the fragmented Empire ' s many warlords and loyalists into a single unified force , Palpatine launched a series of devastating attacks on the New Republic from his new capital at Byss in the Deep Core . With his numbers and also his newly built superweapons , he nearly brought the New Republic to its knees . The Imperial Ruling Council , however , was reluctant to surrender the authority it had gained since Endor . At Sarcev Quest ' s urging the Council had already lent its patronage to Carnor Jax , a Royal Guard officer and aspiring Sith Lord who was to act as a new figurehead for the Empire . Quest and Jax started working together in the heart of the Imperial court to overthrow their Emperor . To lay the groundwork for a coup , Quest installed Carnor Jax as one of the cadre of Imperial Sovereign Protector s who served as the reborn Palpatine ' s personal guard . Together they then sounded out support , eliminating rivals like Sa - Di and Nefta , the only other Force - users on the Council . With funds provided by other Council members , such as Xandel Carivus , Quest bribed the Emperor ' s physician to sabotage the genetic material for the clone bodies which were key to Palpatine ' s rebirth . On the most basic levels the motives of the conspirators are not hard to understand : they were faced with the perceived madness of the Emperor , the transfer of much of their power to a Dark Jedi elite , and the willful , wanton , destruction made by Operation Shadow Hand . Some perhaps believed that they were taking necessary actions for the good of the Empire while others were driven by ambition or concern for their own survival . In any event , the Council now held a dedicated group of conspirators . Jax and Quest led this cabal but the former ' s key role possibly indicates the support of his mistress , the Dark Side Adept Lumiya . The subsequent appearance of Blackhole Stormtroopers as Jax ' s personal guard also hints at a connection with Lord Cronal . Palpatine seems to have been oblivious to the machinations of the Council , and while there is no evidence that they predicted events on Onderon and the destruction of Byss , they were nevertheless ready to make their move when the time was ripe and remove those who might oppose them . After the Battle of Onderon ( Galactic Civil War ) , they orchestrated a coup , headed by those who had regarded themselves as rulers of the Empire and guardians of the principles of the New Order ever since Endor . Daala ' s campaign . Following the collapse of the reborn Palpatine ' s regime , the Empire once again fell into chaos and disarray . High - ranking officials and military commanders gathered their own forces and retreated to the Deep Core , establishing dominions and feuding among themselves for control of what remained . These warlords were self - absorbed beyond anything seen in the post - Endor years with each wasting precious resources in order to advance individual position . Hoping to again reunite the squabbling remnants of the once all - powerful Galactic Empire , Admiral Daala took it upon herself to act as a sort of emissary between the factions . She met with limited success . When Daala was forced into the service of self - titled " Supreme Warlord " Blitzer Harrsk in his fight against High Admiral Treuten Teradoc , she could take it no longer . Allying herself with Teradoc ' s top fleet officer , then - Vice Admiral Gilad Pellaeon , she chaired a meeting at Tsoss Beacon of the thirteen most powerful warlords . Her intent was to negotiate a reunification and the appointment of a Supreme Commander . Hours into the negotiations it became apparent to Daala that the warlords refused to work together . Tired and angry she killed them all by sealing the conference room and poisoning the air . Although it had not been her original intent , Daala effectively made herself both Supreme Commander and Imperial Head of State . The Empire was again poised to wage war against the New Republic . The stable government associated with the Imperial Remnant had not yet been established , but it was this event which began the process by which that government was shaped . Still bitter from the losses she had taken a year prior , Daala regrouped the Imperial Navy under the flag of the Star Dreadnought " Knight Hammer " . She then placed Pellaeon in command of a fleet of seventeen amassed " Imperial " - class Star Destroyers . She also gave control of Crimson Command ( a fleet of one hundred twelve " Victory " - class Star Destroyers ) to Colonel Ivan Cronus , her loyal third - in - command , before setting her plan in motion . In Daala ' s opinion , the greatest hindrance to Imperial victory lay with the Jedi and their academy on Yavin 4 . Focused upon this objective , she ordered Pellaeon ' s fleet to lead the attack as a vanguard for her flagship . The battle was a disaster for the Empire , costing Daala the lives of many loyal soldiers , including Cronus , as well as the " Knight Hammer " . Pellaeon succeeded in recovering Daala from an escape pod , though his Star Destroyers had been damaged by the Jedi . Embarrassed and ashamed , Daala resigned her command and commission ; her final act was to promote Pellaeon to full admiral and convey upon him the powers of Supreme Commander of the Imperial Fleet , thus bringing the Imperial Civil War to an end . Aftermath . The remaining Imperial forces , now known as the Imperial Remnant , suffered several more defeats over the ensuing years , forcing its retreat out of the Deep Core and into eight backwater sectors in the Outer Rim Territories , consolidating new territory carved out of the mini - empires of the galactic fringe such as the Pentastar Alignment . While Pellaeon was not a genius - level strategist like Thrawn , he was an intelligent officer with decades of Navy experience , and what remained of Imperial forces were unified under him . For the next seven years , Pellaeon effectively and efficiently commanded the Imperial Remnant ' s ongoing war against the New Republic , which was proportionately much more costly than it had been when incompetent rival Imperial warlords were fighting each other more often than the rebels . The problem was that the Imperial Civil War had simply done too much damage , with untold numbers of ships lost on infighting and most of the galaxy lost . Even the reunification of the handful of remaining Imperial ships and systems under a capable commander like Pellaeon was too little , too late . Seeing that defeat was imminent , Pellaeon finally admitted the need to sue for peace . After a peace accord was signed with the New Republic , the Remnant settled into a period of stability that was not tested until the Yuuzhan Vong War , when the Imperial Remnant allied with the New Republic and its successor - state , the Galactic Federation of Free Alliances in the fight against the Yuuzhan Vong .