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.
At the close of the Clone Wars, the Separatists on Acherin were in the process of negotiating a peace treaty with the Jedi GeneralGaren 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.[1]
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 AdmiralRiwwel proved too powerful, and, in retribution for his dead soldiers, he razed the remaining resistance stronghold—the capital city Eluthan.[1]
"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."
Although acting Trade Federation ViceroySentepeth Findos had formally dissolved the Trade Federation, others refused to admit defeat. On Enarc, Customs VizierMarath Vooro explicitly denied the authority of Findos and challenged the new Empire with a show of force.[2]
Despite his confidence, Vooro and other Trade Federation factions were defeated by the Empire, ending the Federation permanently.[3]
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 JediMasterDass Jennir, who had survived an assassination attempt on his life during the execution of Order 66 and had subsequently joined forces with the Nosaurians.[4][5]
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.[5]
Gizor Dellso, one of the leading members of the Confederate Remnants.
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.[6]
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.[6]
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.[7]
Above Mustafar, 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. [6]
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.[6]
Early on after the offical 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 near by worlds. In response the Empire sent AdmiralAdar Tallon and GeneralJan 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 on board her flag ship 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.
After the end of the Clone Wars, Separatist forces fled from the worlds of Muunilinst and Mygeeto led by the Muun. These Separatist forces linked up with the Thalassian slavers and other pirates on the world of Vinsoth. The Empire in response to this sent AdmiralTerrinald Screed and GeneralHurst 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.
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.[9]