Confederacy of Independent Systems

The Confederacy of Independent Systems, also known as the Separatist Alliance and simply as the Separatists, was a government in the Outer Rim and separatist movement that stood opposed to the Galactic Republic in the wake of the Naboo Crisis, various planetary and sectorial governments, as well as some mega-corporations, declared intentions to leave the Republic during the Secessionist Movement who refused to comply with its excessive taxation and corruption in the Senate.

Eventually, tensions between it and the Republic developed into war after Anakin Skywalker, Obi-Wan Kenobi, and Padmé Amidala were sentenced to execution on Geonosis and a group of Jedi led by Mace Windu attempted to rescue them. After the Republic revealed its clone army on Geonosis, the Separatists were forced to retreat, beginning the deadly Clone Wars that would devastate the galaxy which was overseen by the Sith.

Background
The origins of the Confederacy can be traced back to Darth Sidious' orchestrated invasion of Naboo by the Trade Federation, in which he was hoping would create a crisis in the Senate. Using the conflict into manipulating the then Queen of the Naboo, Amidala, into calling a Vote of No Confidence against sitting Chancellor Finis Valorum. The vote passed, and in the subsequent election, Sidious&mdash;in his public persona of Palpatine was elected the Supreme Chancellor of the Republic. Secretly, Sidious slowly began exacerbating tensions between the Republic and dissatisfied outlying worlds, eventually forming a Secessionist Movement.

Secessionist Movement
"As I explained to you earlier, I am quite convinced that ten thousand more systems will rally to our cause, with your support, gentlemen."

- Dooku, to the Separatist Council

As the exacerbating political tensions between the Core and Outer Rim systems in the Republic rose as a result of the Invasion of Naboo by the Trade Federation, this made some fear that it would gradually increase to the point where a galactic war was imminent.

The Republic to some had grown so huge and corrupt that any attempt at change required radical thinking and extreme actions. Outlying systems that saw no benefit from being part of the Republic began to rebel after a long history of heavy taxes and indifference from the Core Worlds, who often forced them into accepting one-sided deals and refused to provide military protection. This undercurrent of disgust towards Coruscant was seized by a charismatic leader known as the Sith Lord Darth Tyranus, better known as Count Dooku. The former Jedi rallied together worlds into a Separatist movement that saw the departure of thousands of systems from the Republic. When Dooku's alliance was secretly backed by corporate titans that offered their unlimited droid armies to the cause, the Separatists emerged as a major threat to the Republic. Rebellious activities and political turmoil began on a variety of worlds beginning in outlying Republic star systems that no longer supported the Republic during the Secessionist Movement.

The new Confederacy began to seek to create a southern Separatist sphere of influence. By bringing Yag'Dhul and Sluis Van to his side, Dooku needed to persuade the now prosperous world of Eriadu to join the Separatists. Then Governor Wilhuff Tarkin refused the offer, despite Dooku's commandeering of a HoloNet station in the Raxus system in which he denounced the Galactic Republic.

Meanwhile on the moon of Antar 4, a schism occurred between pro-Galactic Republic loyalists and those who wished to align with the Confederacy of Independent Systems. The loyalists were able to retain power until after the Battle of Geonosis, the first conflict of the Clone Wars, before the moon fell to the Separatist Droid Army.

The Separatist Crisis reached a heightened point as more systems pledged loyalty to Count Dooku and the Confederacy of Independent Systems and a plot to assassinate Senator Padmé Amidala of Naboo was set in motion. Amidala, who was a leading proponent of the Military Creation Act that proposed the creation of an army for the Galactic Republic, was targeted when she arrived on Coruscant for a vote on the measure. The failed attempts were carried out by bounty hunters, Zam Wesell and Jango Fett, who were hired by the Separatists.

Shortly after this, Jedi Knight Obi-Wan Kenobi went on a mission to the aquatic world of Kamino to investigate the identities of those involved in the plot to assassinate Senator Padmé Amidala. Obi-Wan attempted to arrest Jango Fett but failed to do so. Instead, the Jedi Knight tracked his ship, the Slave I to the Outer Rim world of Geonosis where he engaged him in a vicious dogfight. Soon after he landed on Geonosis, Obi-Wan Kenobi was captured and held prisoner after discovering the Confederacy was forming an army to undermine the Republic. However before he was imprisoned by Count Dooku, he managed to send a message to the Jedi Council about his discovery. At Amidala's request, Skywalker attempted to rescue Kenobi, only for both of them to be captured themselves and put in the Petranaki arena along with Kenobi.

During the attempted execution of Jedi Obi-Wan Kenobi, Anakin Skywalker and Senator Padmé Amidala, a team of 200 Jedi was sent to the arena to rescue the trio, but were attacked by a host of battle droids. Jango Fett however was killed while trying to fight Jedi Master Mace Windu after his jetpack malfunctioned. With the battle turning against the Jedi, Dooku gave the remaining Republic forces a chance to lay down their arms, a choice to which Jedi Mace Windu declined. In the next few moments, several Acclamator-class assault ships arrived over the arena, while LAAT/i gunships tore through the droid forces surrounding the Jedi. With the aid of the newly-formed Grand Army of the Republic, the surviving Jedi managed to to escape certain death, all while the newly formed clone troopers engaged Separatist forces on the planets surface, starting the deadly three-year Clone Wars.

Clone Wars
"I have good news for you, my Lord. The war has begun.''" "''Excellent. Everything is going as planned."

- Darth Tyranus and Darth Sidious

Geonosis to Ryloth
"&laquo;The Jedi must not find our designs for the Ultimate Weapon. If they find out what we are planning to build, we're doomed.&raquo;''" "''I will take the designs with me to Coruscant. They will be much safer there&hellip;with my Master."

- Poggle the Lesser and Count Dooku

The arrival of the clones sparked the full-scale battle on Geonosis, with losses on both sides. Poggle ordered his soldiers to retreat and hide, but before he joined them, he turned over plans to the Ultimate Weapon &mdash; a secret project he had been contracted to build by the Separatists &mdash; to Count Dooku. As the battle raged on, Kenobi and Skywalker engaged and were defeated by Dooku in a lightsaber duel before being rescued by Grand Master Yoda. Dooku escaped Geonosis and the Separatists retreated, but the goal of the Sith had been fulfilled; the beginning of the Clone Wars.

Dooku then went to Coruscant, where he met his master in the Works. He informed Sidious that the War had begun, as he had planned. Dooku and his master then recruited the cyborg General Grievous to lead the droid army. At the same time, the Separatists seized control of the major hyperspace lanes following Geonosis, separating the Republic from its army. Ventress, Dooku's apprentice, was sent to assist in helping General Whorm Loathsom during the battle on Christophsis, which at first the Separatist were making gains, but the Republic would end up winning the battle after further reinforcements were dispatched to the planet.

On Teth, Republic forces attempted to save Rotta - the infant son of crime lord Jabba the Hutt - from the Confederacy, who planned to kill the Huttlet and put the whole blame on the Jedi Order. Their aim was to bring the Hutt Clan onto the side of the Separatists in order to access their hyperlanes. However, Jedi General Anakin Skywalker and his Padawan, Ahsoka Tano, were able to rescue the Huttlet from Teth and took him to Tatooine.

Upon the annihilation of the Republic garrison, Ryloth had been completely occupied by the the Separatist Droid Army and Emir Wat Tambor oversaw the occupation from the city of Lessu. He sent his forces to pillage, ravage and rob the Twi'leks' villages and cities of anything valuable.

The Confedaracy used the Malevolence superweapon; which gave them the upper hand against the Republic Navy. This led to encouters over the Ryndellia system, Kaliida Nebula and nearby where its destruction was finally done by the Jedi Order at the hands of Jedi General Anakin Skywalker.

Before the Blockade of Pantora
Malastare was a planet that was a strategic target to the Separatists, as the Republic was also interested in these natural resources. In order to gain the fuel supply-line of the Republic and prevent Malastare from joining the Separatists, they wished to sign a treaty with the Malastare. A T-series tactical droid led the Separatist invasion force, which had almost captured Malastare. In an attempt to turn the flow of the invasion, a Republic superweapon was authorized called the electro-proton bomb, which could release an electromagnetic wave capable of disabling droids and vehicles within an explosive radius. Several Y-wing bombers and ARC-170 starfighters escorted by V-19 Torrent starfighters took off. They maneuvered over the target area and dropped the bomb, in which the ensuing explosion and electromagnetic pulse damaged and deactivated the droid army, along with several Republic vehicles.

The Galactic Republic launched a second major planetary invasion of Geonosis to shut down the Separatist battle droid foundries that Archduke Poggle the Lesser had built there. After their discovery on Cato Neimodia, the Republic dispatched a massive detachment of Clones to retake Geonosis and stop the production of battle droids. After establishing a landing zone at Point Rain near the factories, the Republic disabled the factories' ray shield, making way for the rest of the clone troopers to safely land. As Poggle attempted to retake Point Rain, the main droid foundry was targeted by the Jedi, who battled the droid defenses while others sneaked into the facility via the catacombs beneath it to blow up the facility reactor. They managed to collapse the factory from the inside. Despite the Republic's destruction of other key factories, Poggle remained at large, having escaped his key foundry before its eradication and the crushing defeat for the Separatists.

The Separatists led by General Grievous and Asajj Ventress after the lose of Geonosis launched a daring campaign in the hope of capturing Kamino in order to eliminate the cloning facilities in Tipoca City&mdash; which would mean depriving the Republic from creating more clone troopers for their army and turning the tide of the war in the Separatists' favor. However, they were repelled and driven off Kamino by the Jedi and Republic, despite heavy losses.

The Trade Federation had set up a blockade above the moon Pantora in the Pantora system in an attempt to make them join the Separatist Alliance. As part of the conspiracy to increase pressure, the daughters of the Pantoran Chairman Papanoida were kidnapped who however was able to rescue both daughters and uncover the conspiracy; forcing the Trade Federation to lift the blockade.

Peace Initiative
"Your Republic forces have carried out a barbaric attack on our people! And among the deaths was the very sponsor of the peace accord, Senator Mina Bonteri. With her needless death, I must formally withdraw the proposal for peace offered by our Senate."

- Count Dooku

A peace initiative was created and approved by the Separatist Congress. The motion for a diplomatic end to the war was presented to the Galactic Senate of the Republic who convened an emergency debate to discuss the true cost of the war. However, in light of a recent Confederate terrorist attack and the assassination of Separatist Senator Mina Bonteri, talks would fall apart after senators like Bail Organa, Padmé Amidala and Mon Mothma opposed these views, with Amidala stating that moral responsibility of the war also had to be considered. This triggered accusations of betrayal leading for talks to be halted.

Before the Battle of Mon Cala
"Master, I need your help quickly. I am surrounded.''" "You have already lost the battle, child. I've ordered your reinforcements to return." "No! I will destroy the Jedi. I'll show you!" "''You have failed me for the last time. You are no longer my apprentice. And now, you shall die."

- Asajj Ventress is betrayed by Count Dooku during the Battle of Sullust

The fleet began a major space battle against a Republic flotilla, with Ventress personally leading the Separatists against the Republic. However, the state of the battle would change when Dooku was charged by Darth Sidious with killing Ventress to prove his true allegiance to his Master. Dooku ordered an attempt on his apprentice's life. After recalling Ventress's reinforcements, Dooku had her units directly assaulted and destroyed her Separatist command ship. With the Confederate fleet sustaining heavy damage, Dooku ordered the recall of their armada from Sullust.

Sometime later in and around the Citadel, a Separatist prison on Lola Sayu. A group Jedi and clone troopers led a rescue of Jedi Master Even Piell, Captain Wilhuff Tarkin, and their clone forces. Piell and Tarkin had discovered the coordinates of the hyperspace lane known as the Nexus Route, which they believed could prove vital to the Republic's war effort but the Confedaracy saw it as an chance to change the war in their favour. Though Piell was killed, Tarkin and his forces were rescued and brought the information to the Galactic Republic.

A clash with the Galactic Republic for control of the planet Felucia happened due to the Republic being forced into a retreat at the first battle of Felucia, the Republic re-established a presence and an offensive into Separatist-held territory. In retaliation, General Grievous supplied one of his outposts on Felucia with reinforcements to secure the system for the Confederacy. Responding to the arrival of the battle droid detachment, the Jedi targeted the enemy outpost with each leading a squad to divide the Separatist defenses eliminating all of the droid forces there.

When the Qurren, backed by the Confederacy of Independent Systems, attempted to seize the planet Dac from the Mon Calamari people and the Galactic Republic. The Jedi Order intervened in the conflict, bringing reinforcements from the Grand Army of the Republic and the Gungan Grand Army. However, the Quarren realized that Tamson and Count Dooku were plotting to take Dac only for themselves so they allied with the Republic and routed the Separatists, resulting in Tamson's death.

Alliance with the Zygerrian Slave Empire
The Confederacy had formed an alliance with Queen Miraj Scintel and her slaver empire who wanted to restore it to it formal glory. As part of this plan, they attacked Kiros where the Confederacy supplied them with the captured Togruta population, whom the Zygerrians hoped to sell by bring backing the royal slave auction.

But their plans were foiled by the Jedi who locate the missing colonists, and sent Anakin, Obi-Wan and Ahsoka go undercover to infiltrate the slavers and the auction on Zygerria where they were captured and enslaved. While Scintel develop feeling for Anakin and did not go ahead and kill him which Molec saw as a weakness and invited Dooku to Zygerria to speak with the Queen about her defiance in not killing Skywalker. When the Queen refused, Molec agreed with Dooku about killing the Jedi and that Scintel was unfit to be queen. Molec then stood by as Dooku force-choked her.

The Jedi arrived on the planet on the Zygerrian slave ship Tecora and tried to break into the slave processing facility as the Galactic Republic reinforcements where they battled the slavers where Wolfpack detachment attacked the facility with LAAT/i gunships and clone Z-95 starfighters, but were halted by its ray shields. However, Skywalker was able to destroy the defensive towers, while Kenobi and CT-7567 rebelled and killed Agruss who in a last act, tried to throw the Togruta into the volcanic crevice below the facility, but, following a plan devised by Tano, the Republic forces evacuated everyone onto Admiral Coburn's Arquitens-class light cruiser, the Republic strike team destroyed the slave facility.

Peace Conference
"The Republic recognizes the tragedy of war, but there is nothing we can change that has already occurred.''" "Say it aloud before this gathering&mdash;as representative for Chancellor Palpatine that you declare, without reservation, the Separatist state legitimate''."

- Senators Padmé Amidala and Voe Atell

At the height of the Clone Wars, the Confederacy of Independent Systems held a peace conference with the Galactic Republic on the neutral planet Mandalore between representatives of boty governments in an effort to end the pan-galactic conflict. The conference was presided over by Duchess Satine Kryze within her royal palace in the New Mandalorian capital Sundari. At the beginning of the meeting, Navoo Senator Padmé Amidala opened up the discussions, leading the Republic senators in the peace negotiations, but she was quickly rebuffed by Senator Voe Atell, who called for the Republic to declare the Separatist Alliance legitimate. However, before the delegates could further discuss their terms of peace, Lux Bonteri, son of the late Onderonian senator Mina Bonteri, interrupted the summit and announced to the politicians that it was Count Dooku that had his mother murdered. This led young Bonteri to soon afterward be escorted out by Separatist security droids, allowing the discussion to continue. Shortly after his escape, however, the negotiations fell apart completely.

Onderon Uprising
"Our true king has been silenced. The one you recognize is a traitor and a Separatist minion."

- Saw Gerrera

Having instigated Onderon secession from the Galactic Republic at the war's outset, King Sanjay Rash found his regime, which was being backed by the Confederacy of Independent Systems, challenged by a group of rebels organized by the young insurgent Saw Gerrera. Who hoped to restore the deposed King Ramsis Dendup to the throne. Seeing an opportunity to engage the Confederacy on another front, the Republic bagan to fund the rebels with credits and arms to combat Rash's occupational forces from the Separatist Droid Army. While the Jedi High Council sent a team of advisors to train the rebels along with some of the 501st Legion who were covertly inserted onto Onderon and oversaw training sessions at the insurgency's jungle camp, though the training escalated into actual combat when a battle droid squad attempted to exterminate the rebels, the newly trained rebels eliminated the enemy droid squad and infiltrated the Separatist-occupied capital Iziz, conducting strikes on droid patrols throughout the city and bagan targeting Iziz's main power generator to extinguish the battle droids' recharging source while also proving they were capable of challenging the Separatists and continued offensives against the battle droid forces. Count Dooku sent Rash reinforcements under the command of the super tactical droid General Kalani.

General Tandin and his royal guards sided with the rebels during Rash's attempted execution of ex-King Dendup, helping Steela and her insurgents rescue Dendup and pledging the Royal Onderon Militia to their forces. With Steela appointed by Dendup as their commanding general, the joint rebel and royal soldiers pulled out from Iziz, hoping to preserve civilian lives by isolating armed conflict to the eastern highlands. As full-scale fighting began, the rebels used the mountain terrain against the Separatists and despite heavy casualties, retaliated with a supply of rocket launchers illegally provided by the Republic via the pirate ship Hondo Ohnaka that could penetrate the droid gunships ray shielding allowing the rebelsto win over the Confederate forces, at some point after this final skirmish, Dooku contacted Rash and Kalani. Rash quickly explained what had happened and that they would need even more help to defeat the rebels. Dooku coldly refused, not wanting another war to deal with. He commanded Kalani to call back all of the droid forces from the planet. As Rash angrily protested, Kalani shot the deluded king, killing him. Okalin quickly raised his hands, not wanting to suffer the same fate.

War Deepers
"I've been monitoring your transmissions, General, and I know that this little chat is being sent to the Jedi Council. So let me make one thing perfectly clear. As long as the Republic resists me, 'innocents' will continue to die. Every death in this war lies firmly at the feet of the Jedi. And now&hellip; it is time for you and your passengers to join the ranks of the fallen."

- Dooku chilling words to Chubor before the mass genocide over Mahranee

The Carida Incident was the result of a mission undertaken by the Confederacy of Independent Systems who sabotaged the Venator-class Star Destroyer Renown by loading it with rhydonium canisters with the intention of ramming it into the Valor space station, the site of the Republic strategy conference. While escaping Abafar, the D-Squad took refuge in the Venator-class Star Destroyer, on which they planned to return the stolen Separatist encryption module, but they discovered it was overrun by droids. They undertook efforts to disrupt the Confederate plot and stop the ship from destroying a Republic strategy conference in the Carida system. Separatist and Republic warships would fight over Ringo Vinda for control the ring. The droid army deploying many Battle droids to defend their side of the ring. The Republic came close to taking the ring, attempting to finish off the droids stationed only a few feet away from the separatist control point. The battle ended with a forced retreat from the planet by Republic forces after one of their clone troopers, CT-5385 (nicknamed "Tup") who betrayed and intentionally killed Jedi General Tiplar in a trance-like state. Soon after with their momentum broken, Skywalker ordered a retreat, with Admiral Trench also reporting the odd nature of the victory to Count Dooku, and by extension, Darth Sidious.

Anaxes was attacked by a Confederate fleet under the command of Admiral Trench who besieged the Republic shipyards at Anaxes for weeks on end, exploiting the Techno Union's secret access to a Republic strategy algorithm. Which led to a lengthy campaign. Even as the tide of battle began to turn, Trench remained intent on annihilating the Jedi and their clone infantry. Though he activated a bomb beneath the assembly complex on Anaxes, Skywalker infiltrated Trench's flagship and forced the admiral to divulge the sequence to disarm the device. When Trench tried to retaliate, Skywalker drove his lightsaber through his chest.

The Confederacy would commit a mass genocide under the orders from Dooku of refugees who were escaping from their homeworld of Mahran who were targeted because of its vast resources. The Mahahran people beg for help to the Jedi Order for aid. Jedi General Chubor brought a Galactic Republic task force of clone troopers but they were too late to prevent Confederate forces from laying total waste to the planet capital city. The Separatists did not wish to leave any survivors or witnesses, so Count Dooku outright blamed the Jedi Order for the massacre. It would forced the Jedi Council to lead an operation finally to assassinate Dooku, while refugees alongside the Jedi and clone soldiers fell silent in one of the most deadly actions in the Clone Wars.

Defeating the Shadow Collective
"Maul! Your end is at hand!"

- General Grievous, as the attack began

Darth Sidious brought Maul to the Spire, a prison fortress controlled by the Confederacy of Independent Systems on Stygeon Prime. It was there that Sidious briefly interrogated Maul, and told Count Dooku to find out information about who and where the Shadow Collective leaders were. The goal was to make Maul believe that the Sith wanted to destroy the Shadow Collective, so he would seek out Mother Talzin. Meanwhile, Sidious was followed to Stygeon Prime by two Death Watch warriors, Rook Kast and Gar Saxon, under orders from Mandalore's Prime Minister, Almec to free Maul from the Spire.

After being freed, Maul was tracked to Zanbar by General Grievous along with a Separatist fleet. Dooku ordered Grievous not to kill Maul, simply to defeat and break his forces enough that Maul would seek out Mother Talzin's help. Grievous launched his forces towards the surface, and Maul's troops immediately began firing anti-aircraft weaponry at them. The heavy fire was not enough to repel the ships, however, so the Separatists pressed their attack and deployed all of their forces.

After the Shadow Collective lost on Zanbar, Maul attacked Dooku and Grievous over Ord Mantell which led to Maul make his way into orbit and boarded Grievous' command ship. Grievous disabled the battle droid army after Maul gave him the choice to do so or die, and the cyborg general was taken into custody. Dooku, meanwhile, had engaged and defeated the Nightbrothers in battle, before being captured by the Shadow Collective forces.

Sidious and Grievous arrived to confront Maul and Talzin on Dathomir after finding out where Dooku was being held, the latter of whom had used her magick to take control of Dooku's body. This led to a lightsaber duel, in which Sidious quickly gained the upper hand against the Dooku-controlled Talzin. Talzin appeared in the flesh, returned to her physical form, and held off a Force lightning assault from Sidious and, eventually, Dooku. Talzin sacrificed her own life to allow Maul to escape, as Grievous fatally stabbed the Dathomir witch through the chest while Maul fled from Dathomir. The Separatists, meanwhile, also attacked Maul's Black Sun and Pyke Syndicate allies, leading the mercenaries to end their alliance with Maul; destroying the Shadow Collective.

Final actions
"The end of the war is near General"

- Darth Sidious to General Grievous

Towards the end of the Clone Wars, the Jedi Council decided to assassinate Count Dooku to hasten the end of the war. They sent Quinlan Vos under the guise of a bounty hunter to recruit Ventress, who previously came close to killing Dooku and knew much about him, to aid him in the assassination. Their first attempt on Dooku ended in failure with Vos being captured, with a final plan to assassinate him during the Second battle of Christophsis ending in the death of his formal apprentice Asajj Ventress.

Meanwhile the Republic began laying sieges to many of the Separatist strongholds in the Outer Rim Territories with battles on Cato Neimoidia, Mygeeto, Saleucami, Felucia, and Kaller.

The Separatists led by Count Dooku who had got away from the Jedi on Christophsis, sometime after launched an attack in the Core Worlds on the capital of the Galactic Republic on Coruscant with both the Republic fleets and Confederate fleets fighting over the planet, where Supreme Chancellor Sheev Palpatine was kidnapped by General Grievous, however two Jedi Knights, Obi-Wan Kenobi and Anakin Skywalker were sent to rescue him on board the Invisible Hand. Once onboard and reaching the higher deck, Tyranus laid in wait and dueled the two Jedi Knights, with Skywalker managing to struck down Darth Tyranus during the process at the request of Darth Sidious. After trying to escape, the Chancellor, Jedi, and R2-D2 were captured by Grievous, leading to a second duel. However, Grievous got away and escaped with the Separatist fleet withdrawing, leading the deadly war to carrying on.

Grievous became the de-facto leader of the Confederacy and fled to Utapau after the loss of Count Dooku where he hid till Clone Intelligence found his location, which led the Jedi Order to send Jedi Master Obi-Wan Kenobi to investigate to confirm if there was a Separatist presence, while the Dark Lord of the Sith Darth Sidious ordered that Grievous to send the Separatist Council to the Mustafar system, supposedly to keep them safe from the Republic who was informing the Council of the arrangements as Kenobi overheard secretly.

Meanwhile, hoping to turn the tide of the war, the Separatists mounted an attack on Kashyyyk. This was due to its status as a major navigational point which was of prime strategic importance to the Republic.

Back on Utapau, Obi-Wan confronted Grievous after discovering his presence and shortly after a duel started between the two began, Clones troopers began the fight for Utapau, which would lead to the death of Grievous and warrant a final blow to the Separatist Alliance.

Fall of the Confedaracy
"The Separatists have been taken care of, my master.''" "''It is finished, then. You have restored peace and justice to the galaxy."

- Darth Vader and Darth Sidious

Massacre on Mustafar
"The plan has gone as you had promised, my Lord.''" "''You have done well, Viceroy. When my new apprentice, Darth Vader, arrives, he will take care of you."

- Nute Gunray and Darth Sidious

The Separatist Alliance had been defeated by the Republic just as Darth Sidious had intended; with it final losses on Kashyyyk and the Outer Rim Territories during the Sieges and the death of General Grievous, ending the fighting shortly after. With the Separatists still in control of their assets and remaining worlds, the Chancellor of the Republic sent his new enforcer to deal with the last threat to his vision.

In the final act of the Sith grand plan; the Separatist leadership was murdered by the Sith Lord Darth Vader in their bunker within the mineing complex on Mustafar, with Nute Gunray the last to fall, officially ending the Separatist cause and with Vader receiving the order to end the Clone Wars by sending a shutdown signal to the entire droid army and navy, without them to protect the remaining Separatist planets. They were forced to surrender to the Empire and live under Imperial rule, which was all a pretext to amassing complete central authority over the Republic, so it could be transformed into the First Galactic Empire.

Subjection of Separatist worlds
"As Governor Tarkin can attest, our navy was still chasing Separatist holdouts as late as a year ago."

- Rancit, to Tarkin

Following the fall of the Confederate leadership on Mustafar and the destruction of the complex during a duel between Darth Vader and Obi-Wan Kenobi after, the fledgling Empire rooted out remaining Separatist holdouts for at least four years after the Clone Wars, while criminal organizations composed of re-purposed battle droids such as the Droid Gotra operated in Coruscant's underground.

Seeking to make examples of worlds who continued to harbor secessionist tendencies, worlds like Kooriva, Murkhana and Raxus, which still hosted ex-Separatists, became a target of the Empire, with one year after the end of the Clone Wars then Moff Wilhuff Tarkin was assigned to make an example of Antar 4, a populous moon that had been a part of the Confederacy of Independent Systems. Wanting to make examples of worlds who continued to harbor secessionist tendencies, Imperial forces however made no attempt to sort the Separatists from Imperial loyalists when they carried out mass arrests, executions, and massacres. This served to compel Raxus and other worlds to surrender all former Separatists to Imperial custody, or else suffer a similar demise to that of Antar 4.

The Empire would later see to the near-extermination of all life on Geonosis, a once major Separatist world, by wiping out most of the entire population of Geonosians using bombs and other foreign weapons.

Legacy
"Understand as a Separatist, I fought for freedom but put my trust in a corrupt leadership." "You were the leadership—a General." "The Jedi were Generals. Do you truly believe they comprehended the cause they started? Holster your weapon, boy. We are no longer enemies. Perhaps we never were."

- Former Separatist General Kleeve to Jedi survivor Caleb Dume

In the time of the Galactic Empire, it used the memory of the war to maintain order, telling the galaxy that it was the rebellious Separatists that caused the destructive Clone Wars. The term "Separatist" was used to refer generally to those still involved in forming rebellion. Separatist military equipment and technology that survived the Clone Wars continued to be in use by varying resistances and pirates that managed to obtain them for their own purpose, with some being reused and modified extensively by the Alliance to Restore the Republic, such as the IG-227 Hailfire-class droid tank and Armored Assault Tank during the Galactic Civil War.

Soon after the Empire's formation, Emperor Palpatine and Darth Vader observed the construction of the Death Star, which had begun construction sometime during the Clone Wars by the Confederacy, having partially completed a framework by the time the war came to an end. With the Separatists defeated and their leaders killed, the Ultimate Weapon project was appropriated by the nascent Galactic Empire, who planned to use it to control the galaxy. Nineteen years later, the Death Star was used to destroy the planet Alderaan, killing millions of people living there, and later was destroyed in the Battle of Yavin by a young Rebel pilot and the son of Darth Vader, Luke Skywalker.

Military
"Our friends from the Trade Federation have pledged their support. And when their battle droids are combined with yours, we shall have an army greater than any in the galaxy. The Jedi will be overwhelmed. The Republic will agree to any demands we make."

- Count Dooku

The various commercial entities who joined under the banner of the Confederacy pledged their forces to the Separatist Army, creating one sprawling group of droids as well as organic forces, and local warriors, and was often referred to as the Droid Army. These ranged from the Trade Federation's battle droids to the security forces maintained by the Commerce Guild, InterGalactic Banking Clan and Corporate Alliance.

One of the largest contributions was by the Techno Union, which donated not only its new B2 super battle droids, but numerous foundries capable of producing thousands more droids for the Confederacy.

It also deployed much larger weapons of war during the Clone Wars. Commerce Guild OG-9 homing spider droids were a common sight on many frontlines, and tank droids, droid subfighters, and AATs provided heavy firepower.

Astrography
The territory of the Confederacy of Independent Systems varied in size a great deal during the course of its short history numbered at least ten thousand star systems, as well as the various commercial groups with the planets they controlled. Theses systems mostly fell to the Galactic Republic during the Clone Wars. With the remaining fell under the rule to the Galactic Empire shortly after the war ended.