The Separatist holdouts consisted of various disparate fragments of the Confederacy of Independent Systems that remained active after the execution of the Separatist leadership at the end of the Clone Wars, trying to preserve their New Order. The Galactic Empire used the existence of such holdouts as one of several excuses to continue production of various warships for the Imperial Navy.
With the death of the Separatist leaders at the hands of Darth Vader, the deactivation of the majority of the Separatist droid armies, the dissolution of the Confederacy's major commercial organizations, and the surrender of almost all remaining Separatist planets and forts, the Confederacy of Independent Systems effectively ceased to exist. With both the Sith Master and the Sith apprentice having betrayed the Confederacy, its leaders were reduced to various Warlords. However, various small remnants, like the Trade Federation resistance, managed to survive.
- "We didn't dare to hope that we'd beat them. We hoped we would be enough of a nuisance that they'd just go away."
At the close of the Clone Wars, the Separatists on Acherin were in the process of negotiating a peace treaty with the Jedi General Garen Muln. After Muln survived an assassination attempt made by his own clone troopers when Order 66 was initiated, the Acherin Separatists retreated to their fortified cities, hid the Jedi until he could be evacuated off-world, and declared war on the emerging Galactic Empire.
For nearly a year, the Separatist resistance managed to keep the Empire at bay, in a war that inflicted great casualties on both sides. In the end, the forces of Admiral Riwwel proved too powerful, and, in retribution for casualties sustained during the campaign, he razed the remaining resistance stronghold—the capital city Eluthan.
The Reconquest of the RimEdit
The majority of Separatist holdouts were dealt with by the Empire between 19 and 17 BBY in the Reconquest of the Rim, a massive military campaign aimed at restoring order and establishing Imperial control in the Outer Rim Territories.
Early on after the official end of the Clone Wars, an army and navy of still-active battle droids came under the control of former senator Toonbuck Toora. Toora used these forces to conduct a campaign of resistance against the newly formed Galactic Empire. She fortified her homeworld of Sy Myrth and captured several nearby worlds. In response the Empire sent Admiral Adar Tallon and General Jan Dodonna to deal with the holdout. After a string of losses for Toora, she was finally cornered over the planet Trasemene and a bloody battle ensued in which Toora died aboard her flagship Defiance's Banner. All the remaining Separatist forces loyal to Toora were destroyed in the battle along with their leader, ending Separatist resistance in that region of space.
A handful of Separatist survivors fled into the Kreetan Narrows after the defeat and continued a low-level resistance, leading to the Empire's eventual annexation of the region and the northern territories of Hutt Space.
After the end of the Clone Wars, Separatist forces led by the Muuns fled from the worlds of Muunilinst and Mygeeto. These Separatist forces linked up with the Thalassian slavers and other pirates on the world of Vinsoth. The Empire in response sent Admiral Terrinald Screed and General Hurst Romodi, and the two beat the Separatists off Vinsoth. After this loss the Muun leadership dug in on the planet Binquaros and sent their fleet to Bimmiel. Romodi began to grind down the holdouts on Binquaros while Screed shredded the Separatist fleet at Bimmiel. While all this was going on, a group of pirates and Mandalorians who had been pushed from the Salin Corridor broke through Screed's rear guard and beat Romodi on Binquaros, freeing the Muun. This new force fled for the Unknown Regions but it was intercepted in the Vardoss system and crushed.
- "Where is Gunray? Where is Haako? A third-tier flunky has no right to negotiate on the Trade Federation's behalf. We have our battleships. We have our droids. If Palpatine wants our wealth, let him come and take it."
- ―Marath Vooro
Although acting Trade Federation Viceroy Sentepeth Findos had formally dissolved the Trade Federation, others refused to admit defeat. On Enarc, Customs Vizier Marath Vooro explicitly denied the authority of Findos and challenged the new Empire with a show of force. Despite his confidence, Vooro and other Trade Federation factions were defeated by the Empire, ending the Federation permanently.
In 18 BBY, The Bothan sector was reportedly invaded by Aqualish separatists that allied with Harch raiders. They managed to control the worlds of Nooli and Galboron. In response, the Empire sent Captain Par Lankin who managed to liberate the entire sector that same standard year.
The Western Reaches OperationEdit
In 17 BBY, Separatist forces under General Kendu Ultho linked up with Iska pirates and managed to maintain control within the sectors until the Empire sent Grand Moff Wilhuff Tarkin to liberate those systems that same year. Separatist forces used organic-accompanied vulture-droid starfighters along with Z-95 Headhunters against the Imperial Navy but all efforts were lost as all ninety-five systems and eight sectors were eventually liberated and brought an end to the separatist influence over that region.
- "I would not throw my life away so hastily—or so vainly—but neither am I done fighting for the principles on which the Republic was based."
- ―Dass Jennir
On New Plympto, the Nosaurian Separatist army fought on against the Empire, even as their chances of winning slimmed each day. They were led by the Jedi Master Dass Jennir, who had survived an assassination attempt on his life during the execution of Order 66 and had subsequently joined forces with the Nosaurians.
The fighting continued for a month, eventually leading to the 501st Legion being sent to assist the Imperial force in ending the uprising. At the Battle of Half-Axe Pass, the last fragment of the Nosaurian army was destroyed, with the surviving soldiers being slaughtered. Only Jennir and Bomo Greenbark survived the massacre.
- "Once we arrived on the molten surface of Mustafar, it soon became apparent Dellso had been a busy little bug."
- ―Anonymous 501st stormtrooper
Another Separatist to resist after the Clone Wars was Gizor Dellso. Having arrived on Mustafar some time after the assassination of the Separatist Council at the end of the war, Dellso discovered the remains of his former master, Poggle the Lesser, and the others in the control room of the mining complex.
Dellso remained in denial that the Clone Wars were over, and, being the creator of the Separatist Droid Army signal beacon, reactivated a secret droid factory hidden near the mining facility, building his own private droid army. Becoming the leader of at least one Confederate remnant, Dellso stayed on Mustafar, plotting to overthrow the Galactic Empire.
In the meantime, the Empire tracked down remaining Separatist strongholds and hideouts, either forcing their surrender or destroying them outright—sometimes even using their own hardware against them, such as reprogrammed DSD1 dwarf spider droids and droidekas.
By 12 BBY, Dellso and his entourage of Geonosian officers had amassed a fleet of starships in readiness for his new campaign against the Empire and had the droids to man them, as well as re-activated droid starfighters. Dellso also discovered old battle droid data stored in the data computers of the surface complex and made provisions to manufacture the experimental droids. This next generation battle droid was to have become a major addition to the Confederacy, but the government was dissolved before production began. Adding to his peril, Dellso was also in possession of sensitive Imperial data, pertaining to a new starfighter the Empire was intending to have built. 
Eventually revealing themselves to the Galactic Empire, Darth Vader tracked Dellso's fleet back to Mustafar, where he dispatched the 501st Legion to put down the last remnants of the CIS, once and for all. The Empire established orbital positions, and continued to lay siege to Mustafar. The engineers of the 501st destroyed the experimental droid schematics and planted an orbital beacon in the droid factory while engaging the enemies they had thought they would never see again. Meanwhile, Dellso and his officers desperately launched attacks on the Imperial forces. However, they were all eventually killed, and the factory was destroyed by an orbital bombardment along with the Geonosian Industries.
The Alliance and SeparatismEdit
Following the signing of the Corellian Treaty and the Declaration of Rebellion in 2 BBY, most Separatist holdouts that had survived 17 years after the Clone Wars' end, such as the Bryx Freedom Fighters and Separatist prisoners of Kota's Militia, were absorbed into the Rebel Alliance, although certain former Separatists such as the Neimoidian Captain Blox Hatha were refused membership into the Rebel Alliance owing to previous war crimes. Even with this setback, Blox flew a privateer vessel in support bearing a Rebel letter of marque and reprisal. The Rebels managed to get their hands on Separatist war material, such as Lucrehulk-class battleships, Recusant-class light destroyers, Providence-class carrier/destroyers and Munificent-class star frigates. Many surviving frigates had roamed the galaxy for years, with their old crews serving as mercenaries or pirates. They modified their vessels to such an extent that many were unrecognizable from their original configuration. As such, they went well with the rag-tag look of the early Alliance Fleet.
During the Imperial Period, a group known as the Bryx Freedom Fighters in the Bryx sector led by General Horn Ambigene remained partial towards the Separatist cause even after the Confederacy's fragmentation. They played multiple roles in resisting imperial forces over their sector until they were later reorganized with the Alliance to Restore the Republic in 2 BBY.
Despite the gradual dissolution and/or incorporation into the Rebel Alliance of surviving Separatist holdout forces, Imperial officers like Conan Antonio Motti still referred to Separatism as a current threat, alongside rebels and criminal enterprises, as late as 1 BBY.
Stragglers on TatooineEdit
Several Separatist droid pods crashed-landed into the mountains near Mos Eisley on Tatooine. In 1 ABY, there were still pockets of battle droid survivors that did not respond to the shutdown and were left in a frenzied state. Several spacers were tasked with recovering parts from the escape pods and were met by fire by these error-prone droids. The spacers however succeeded and left the remaining battle droids to fend for themselves in the harsh elements.
Experiments on LokEdit
Several pods made their way in the barren deserts of Lok as an experiment conducted by the Trade Federation. These pods carried numerous amounts of glitched droidekas that did not respond to the shutdown. As of 1 ABY, these droidekas were still functional. Many of these same units took refuge in a nearby cave where they massacred almost all the miners and left the cave poisoned and barely reachable by any outsider.
Nuisance on KashyyykEdit
On Kashyyyk, a few battle droids and droidekas left over from the Battle of Kashyyyk ignored the shutdown signal and were left active for decades in the Shadowlands. In 1 ABY, A few spacers were tasked with destroying these battle droids as they had become a threat to the wildlife and the Wookiee hunters that used this desolate territory.
Leftovers on GeonosisEdit
On Geonosis, a number of droids left behind from the Original Battle of Geonosis did not respond to the shut-down order but continued functioning for several decades. These droids managed to survive in functional condition inside undiscovered pockets of Geonosis's canyons, all the way into the Galactic Civil War, along with other relics from the Clone Wars, such as a Lucrehulk-class core ship.
In 3 ABY, the droids opened fire on Imperial detachments that crashed into the trenches in escape pods during a space battle above the planet. Most of the stormtroopers were overwhelmed and killed. A Rebel pilot, Wedge Antilles, was forced to crash-land on the planet after losing his starfighter's stabilizers. Antilles managed to wipe out the remaining stormtroopers and nearby battle droids before escaping the world in a modified Delta-7 that he found, making good use of its seismic charges against Imperial forces.
Relics on HyporiEdit
On Hypori, multiple templates of Droideka Mark IIs were left behind in a hidden droid foundry on Hypori to serve as automated defenses. In 3 ABY, Tyber Zann and Urai Fen found word of the abandoned factory and decided to infiltrate the facility. They were ambushed by droidekas and had to battle their way deeper into the facility for Urai Fen to turn the factory security off. Bossk attempted to capture Tyber but was later persuaded to join his cause for the consortium. Jabba the Hutt and his forces arrived to capture the foundry which sent the trio to reprogram the factory security to fight for the consortium. Outnumbered and outmatched, Jabba conceded and gave Tyber the facility along with the rest of the planet.
Outbound Flight RecoveryEdit
The Outbound Flight was an expedition voyage that launched in 27 BBY and attempted to make several colonizations in the Outer Rim. The project was sabotaged by Chancellor Palpatine when he sent a Trade Federation taskforce of vulture droids, battle droids, and droidekas. Outbound Flight was severely damaged by a Chiss fleet under the command of Commander Thrawn, all of the colonists and Jedi in the Dreadnaughts died in radiation explosions. However many colonists and the Jedi Lorana Jinzler survived in the central storage area. Lorana Jinzler and Thrass (the brother of Thrawn) crash landed and unfortunately died in the attempt. The vessel had crashed on The Redoubt and the colonies were nevertheless created. Luke Skywalker and Mara Jade Skywalker discovered the wreckage in 22 ABY. They were met under fire by an aged droideka that failed to respond to the shutdown in 19 BBY. Both Jedi had trouble with the droideka but eventually destroyed it along with any last remaining relics of the Federation and Separatist influence.
Military and war materialEdit
The military of the various Separatist remnants usually—but not always—consisted of droid and ship models that had been used in the Separatist Droid Army and the Confederate Navy. The ground units included B1 battle droids, B2 super battle droids, droidekas, IG-100 MagnaGuards, and Heavy Missile Platforms. Geonosian warriors were also a part of at least one faction. Aqualish soldiers were mentioned fighting and leading battles against the Empire during several reconquests and sieges. The navies consisted of primarily Providence-class carrier/destroyers, Lucrehulk-class battleships, and Munificent-class star frigates for support. The holdout navies retained most of the CIS's major starfighters, such as Vulture droids and droid tri-fighter.
- Republic HoloNet News Special Inaugural Edition 16:5:241
- The Order of Outcasts
- Republic 80: Into the Unknown, Part 2
- Dark Times 1: The Path to Nowhere, Part 1
- Dark Times 2: The Path to Nowhere, Part 2
- The Last of the Jedi: Dark Warning
- "The Guns of Kelrodo-Ai"—Star Wars Insider 132
- Star Wars: Battlefront II
- Star Wars: Rogue Squadron III: Rebel Strike (First appearance)
- Star Wars Battlefront: Elite Squadron
- Star Wars: The Force Unleashed II (Indirect mention only)
- Star Wars Galaxies: An Empire Divided
- Star Wars: Empire at War: Forces of Corruption
- Star Wars: Rebellion (comics)
- Starships of the Galaxy (Saga Edition)
- The Complete Star Wars Encyclopedia
- The Essential Guide to Warfare
Notes and referencesEdit
- ↑ 1.0 1.1 The Last of the Jedi: Dark Warning
- ↑ Republic HoloNet News Special Inaugural Edition 16:5:241
- ↑ The Complete Star Wars Encyclopedia
- ↑ Republic 80: Into the Unknown, Part 2
- ↑ 5.0 5.1 Dark Times 1: The Path to Nowhere, Part 1
- ↑ 6.0 6.1 6.2 6.3 Star Wars: Battlefront II
- ↑ Star Wars: Revenge of the Sith The Visual Dictionary
- ↑ Starships of the Galaxy (Saga Edition)
- ↑ The Essential Guide to Warfare
- ↑ 11.0 11.1 11.2 Star Wars Galaxies: An Empire Divided
- ↑ 12.0 12.1 Star Wars: Rogue Squadron III: Rebel Strike