Separatist holdouts

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 the latter ultimately lost, 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 in the Western Reaches. These holdouts varied from groups of pro-Separatist sentients to battle droids that did not follow the shutdown command at the end of the Clone Wars, which could be mostly independent and disconnected from each other. Commander Orson Callan Krennic claimed the Separatist holdouts were mere-anarchists who hoped to bring down galactic civilization, although Krennic claimed as such while he was trying to persuade his old friend Galen Walton Erso to help the Empire.

Governor Tawni Ames of the Desix Separatist holdout fought the Empire in the name of maintaining her people's freedom. Surviving battle droids followed their pre-existing programming or fought under surviving organic Separatists and any surviving tactical droids, whose programming also remained pro-Confederate despite the government's defeat. The ST-series tactical droid Kalani further hoped to find a way to end the Clone Wars in a Separatist victory. While Kalani was open to peace with the Empire, he ultimately came to the conclusion that, as the successor to the Republic, it was his enemy. Ames's Desix holdout had come to a similar conclusion, with Ames herself believing the Empire was the worse form of the Republic Count Dooku had predicted. Ames was open to laying down her arms to open diplomatic talks and avoid another war, as proposed by Clone Commander Cody, but Imperial governor Grotton did not honor Cody's offer. Kalani himself would ally with the Spectres rebel group upon realizing they had a common enemy in the Empire, coming to terms with the Clone Wars's end in the process, but parted ways with the rebels rather than join the Phoenix Cell.

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 ultimately executed the council and deactivated 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 sectors 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.

Early into the Empire, the war was not entirely over, as some pockets of resistance rebelled against the new government. Hardline Separatists entrenched themselves in the Corporate Sector, the Western Reaches, and the Tion Hegemony, which was where the former Separatist capital planet, Raxus Secundus, was located. Raxus itself, however, would quickly fall under Imperial occupation. 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 Raxus. The Kelrodo-Ai holdout was active and deployed at least one Variable Geometry Self-Propelled Battle Droid, Mark I.

Senator Avi Singh of Raxus was persuaded by the Empire to endorse Captain Bragg's occupation, only to reject the occupation and escape the planet with Clone Force 99. Part of the reason the Onager-class Star Destroyer was developed was so the Empire could ruthlessly take out the planetary shields used by CIS holdouts. Governor Tawni Ames and the people of the planet Desix refused to bow to the Empire and resisted its occupation, deploying a force of reactivated battle droids in the process. However, a clone stormtrooper squad infiltrated Desix City and overthrew her holdout, with clone commando Crosshair executing Ames herself despite Clone Commander Cody's desire for peace.

The Empire would justify the construction of Imperial-class Star Destroyer due to its never-ending need to fight Separatist holdouts. In 18 BBY, the Empire oversaw a campaign of mass arrests, executions, and massacres on Antar 4 overseen by Wilhuff Tarkin that swept up many republic loyalists. 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 cadets. Zare Leonis imagined serving the Empire; fighting against Separatist holdouts, pirates, and enslavers.

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 shipyards like the one in orbit over Kartoosh, just outside of the Western Reaches, served as a repair hub for starships damaged in engagements with Separatists as well as salvage yards 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 Palpatine himself.

Both Tarkin and Lieutenant Commander Orson Krennic would also utilize the conflict against the holdouts as a pretext to justify for the appropriation of numerous legacy worlds—worlds legally protected as ecological reserves—advancing the top-secret Imperial construction project occurring above Geonosis. The same year, Moff Tarkin was reassigned to Sentinel Base to oversee the Death Star project. Many in the Imperial hierarchy wrongly believed that this was because of a failure commanding the mop-up operations. 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.

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 during the days of the early rebellion against the Galactic Empire, one holdout was encountered by the Republic Clone Wars veteran, Captain Rex, while leading a rebel cell from Lothal on a mission to Agamar to salvage proton bombs from a derelict DH-Omni Support Vessel. 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, Bridger 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.

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 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-series 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-series super battle droids on board to stop the intruders, believing that they were Republic clone troopers. 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, Ithano's crew, now joined by Kix, went to seek further raids of Separatist locations. One of these holdouts was located on a swampy 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 referenced this story to some visitors by describing it as "spooky."

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