Separatist holdouts Separatist holdouts was a term for the collective military and political segments of the Confederacy of Independent Systems , an government of star system s and corporations that seceded from the Galactic Republic . The Separatist holdouts came to exist as remnants of the former Confederacy in the aftermath of the Clone Wars , a pan - galactic civil war that was fought between the Republic and Separatists from 22 BBY to 19 BBY . During the subsequent era known as the Age of the Empire , the Separatist holdouts were hunted by the Republic ' s successor , the Galactic Empire . During the rebellion , they helped a group of rebels against the Empire . Description . Separatist holdouts were the remnants of the Confederacy of Independent Systems . The political crisis between the Galactic Republic and the Confederacy culminated in the Clone Wars , a galaxy - wide conflict that was ultimately lost to the latter , yet also allowed the Galactic Empire to rise in place of the Republic . Although the war ' s conclusion marked the end of the Separatist cause , the remnants of the Confederacy would endure for years , hiding from the New Order in several locations such as the planet Agamar or the Western Reaches . These holdouts varied from groups of pro - Separatist sentients to battle droid s that did not follow the shutdown command at the end of the Clone Wars which were mostly independent and disconnected from one and another . History . Origin . By 19 BBY , the last year of the Clone Wars , the highest ranking leaders fell in quick succession ; beginning with Confederate Head of State Count Dooku , who was killed during the raid over the Republic ' s capital world of Coruscant and General Grievous , perished on Utapau while trying to escape . The Separatist Council , including Viceroy of the Trade Federation Nute Gunray , retreated to Mustafar . As the war drew to a close , Supreme Chancellor Sheev Palpatine — secretly Darth Sidious , the Dark Lord of the Sith — declared himself Emperor and transformed the Galactic Republic into the Galactic Empire . Having gained absolute power through the conflict , the Emperor dispatched his new apprentice , the Sith Lord Darth Vader , under the pretext of peace to Mustafar where he would ultimately execute the council and deactivate the majority of the Separatist Droid Army instead , bringing an end to both the separatists and the Clone Wars . As a result , most of the remaining systems and sector s in the Confederacy fell to the power of the Galactic Empire and were occupied shortly after . However , some of the military and governing elements began retreating to the Western Reaches to continue their resistance while others such as General Kleeve abandoned the Confederacy altogether . Resisting the Empire . The early years of the Empire were marked by the military occupation and subjugation of various worlds that were part of the Confederacy , including Kooriva , Murkhana , and the former capital planet , Raxus . In 18 BBY , the Empire oversaw a campaign of mass arrests , executions , and massacres on Antar 4 overseen by Wilhuff Tarkin . Two reporters , Anora Fair and Hask Taff , reported heavily on the operation , angering prominent Coruscanti and causing considerable political controversy . Despite this , the Empire continued to utilize the existence of Separatist holdouts as an excuse for its continued peacetime military expansion and to justify increasing security measures . With booming civic pride and patriotism , many galactic citizenry joined the Imperial Military as Imperial cadet s . Zare Leonis imagined serving the Empire ; fighting against Separatist holdouts , pirate s , and slaver s . Soon after , the Imperial Navy proceeded to mount incursions into holdout - held space , including a series of campaigns in the Western Reaches , where most of what was left of the Confederacy of Independent Systems had fled . As the conflict progressed , the planetary populations of former Confederate worlds , dissatisfied with the Empire ' s perceived lack of reconstructive action in the Clone Wars ' aftermath , only added to the holdouts , further swelling their numbers . Imperial shipyard s like the one in orbit over Kartoosh , just outside of the Western Reaches , served as a repair hub for starship s damaged in engagements with Separatists as well as salvage yard s for captured vessels . The Bilbringi shipyards also served as a dismantling point for old Separatist warships . The Imperial forces were led by Moff Wilhuff Tarkin , fresh from " pacifying Antar 4 , " who had been assigned to oversee operations by Emperor Sheev Palpatine himself . Both Tarkin and Lieutenant Commander Orson Krennic would utilize the conflict against the holdouts as a pretext to justify for the appropriation of numerous legacy world s — worlds legally protected as ecological reserves — advancing the top - secret Imperial construction project occurring above Geonosis . In 18 BBY , Moff Tarkin was reassigned to Sentinel Base to oversee the Death Star project . Many in the Imperial hierarchy believed that this was because of a failure commanding the mop - up operations , despite the conflict in the Western Reaches being considered over by 15 BBY . However , two years later , Separatist holdouts were still viewed as a major threat by the Imperial Military , and were thus initially suspected of being culpable for the attack on Sentinel Base . Age of rebellion . Separatists who did not relinquish the struggle against the Galactic Republic and its successor , the Galactic Empire , were natural allies of the growing rebellion . These " diehard " Separatists were , however , more fanatical than other rebels and had a higher degree of willingness to undertake radical measures against the Empire than the politically astute leaders of the central resistance are restful for . There were many instances where the Separatists were former soldiers or operatives , as the droid members of the formerly extensive Separatist Droid Army were inoperable and rarely joined resistance groups . These Separatists were experienced with military or sabotage training , and had recruited family or younger individuals as most were typically older . Several knew of forgotten Separatist bases or weapons stockpiles . Characteristically , Separatists fought as individuals , yet in instances of extensive local resistance they were able to conjure forces that rivaled those of the nascent rebellion . In 2 BBY , one holdout was encountered by retired Clone Captain Rex while leading a rebel cell from Lothal on a mission to Agamar to salvage proton bomb s from a Separatist crash site . Rex along with Jedi Knight Kanan Jarrus , Padawan Ezra Bridger , and Garazeb Orrelios were quickly captured by General Kalani , a high ranking super tactical droid of the Confederacy military . Kalani , having studied the tactics of the war for over a decade , forced the rebels to take part in a final combat simulation designed to prove once and for all which side had the better combat strategy . However Ezra managed to convince Kalani that neither the Republic nor the Separatists really won the Clone Wars , but had both been decimated by their true enemy : the Empire . Due to collaboration between the rebels and former separatists , Kalani and the rebels were able to mount a successful rearguard defense against an Imperial attack . General Kalani and the rebels ultimately escaped aboard Neimoidian " Sheathipede " - class transport shuttles . Refusing an offer to join the rebellion , Kalani shared his prediction that the rebels had a 1 % chance of success against the Empire before departing to parts unknown . Saw Gerrera and a team of his Partisans encountered several battle droids on Geonosis in 2 BBY . These battle droids were used by one surviving Geonosian , Klik - Klak , to protect himself and his Queen egg . Klik - Klak also used several destroyer droids to protect a old separatist shield generator . After taking out Gerrera ' s team , Captain Rex and the Spectres arrived to find Gerrera . After destroying the battle droids , Bridger and Chopper subdued Klik - Klak and deactivated the remaining droids . Legacy . In 31 ABY , fifty years after the Clone Wars , a discounted holdout continued to exist due to an ion storm striking the cruiser " Obrexta III " decades earlier . The cruiser was tasked with carrying the captured clone trooper CT - 6116 from the planet Coruscant to Serenno , and had him locked in a cryo - cycle stasis pod . En route , the cruiser had been attacked by Republic forces and heavily damaged . Knowing that the ship was in no shape to reach Serenno , B1 battle droid B1 - CC14 activated the ship ' s emergency beacon before jumping the ship to a random point through hyperspace . The jump took it to the desert planet Ponemah Terminal in the Outer Rim , where it fell into the planet ' s surface and B1 - CC14 lost power . Decades later , the cruiser would have some of its systems re - powered , including its emergency broadcast . Believing the " Obrexta III " contained the legendary lost treasure of Count Dooku , a number of pirate groups raced to the downed ship . After one group of pirates led by Sidon Ithano managed to get aboard the vessel , B1 - CC14 , unaware that Clone Wars were long over , briefly powered back up and activated a fail - safe that would mobilize all B2 super battle droid s on board to stop the intruders , believing that they were Republic clone trooper s . As the pirates tried to escape , the battle droid was ultimately destroyed as the " Obrexta III " exploded . Having recovered CT - 6116 from cryo - cycle stasis , the crew of the " Meson Martinet " offered the clone to join their crew scouring the galaxy for lost Separatist installations they had discovered with the recovery of the " Obrexa III ' s " memory core , which he humbly accepted . After the incident , Sidon Ithano ' s crew , now joined by Kix , went on further raids of Separatist holdouts . One of these holdouts was located on a swamp y misty planet , where B1 battle droids came up from the ground to attack the crew , which included Ithano himself , Kix and Reveth . C - 3PO later retold this story to some visitors and described it as " spooky . "