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The Confederacy of Independent Systems was the government of the separatist movement publicly led by Count Dooku (and secretly led by Darth Sidious). The Separatists are the main antagonists of the prequel trilogy and Star Wars: The Clone Wars.
Sometime after the Clone Wars ended; Palpatine dissolved the Confederacy of Independent Systems and reorganize it into the Galactic Empire.
Despite it's brief existence, the Confederacy left a lasting effect on the Galaxy. It's existence lead to the Clone Wars which lasted for three years and enabled Darth Sidious to bring about the Revenge of the Sith and the Birth of the Galactic Empire both of which enabled the Sith Order to rule the Galaxy for twenty-three years. Archduke Poggle the Lesser had the first Death Star's plans created. The war legalized the Clone Troopers who after the War became the first Imperial Stormtroopers. The War turned public opinion against the Jedi Order so completely that after 99% of the Jedi Order were wiped out during the Execution of Order 66 the Emperor was able to have the remaining Jedi declared enemies of the state just like that. It also turned public opinion against the alien species of the galaxy so completely that the Emperor was able to repeal all of the Old Republic's anti-slavery laws and turned every alien species starting with those the leaders of the Sepratist Council belonged to into slave labor most of which was used during the construction of the first Death Star. It also left the Galactic Public so war-weary that the reason the was no open rebellion except for a few resistance movements on Kashyyyk and Ryloth is because the large majority just didn't care that the Republic and the Jedi Order were gone and that slavery had reemerged in the galaxy to the point where those who did care could not rally enough support to do anything about it. This forced the remaining Jedi to go into hiding and Bail Organa to work against the Emperor in secret. CIS technology was salvaged by the Wookies to repeal Darth Vader's task force on the hunt for the lost Jedi during the Subjugation of Kashyyyk leading to Vader ordering a full planetary bombardment and completing his transformation from a Jedi Knight into a Sith Lord. It also lead to the creation of the Imperial Inquisition.
Formed by various planetary and sectorial governments, as well as the economic cartels like the Trade Federation, the Confederacy declared intentions to leave the Galactic Republic because of its excessive taxation and the corruption in the Senate.
What no one but Dooku knew was that the Separatist Crisis and the Clone Wars that followed were all part of a plan by Darth Sidious to execute Darth Bane's grand plan: the Revenge of the Sith and the birth of a new Sith Empire.
For three years, the Clone Wars raged across the galaxy while, in his public persona as Surpreme Chancellor Sheev Palpatine, Sidious used the war to increase his popularity and his political, economic, and military power via his emergency powers. Meanwhile, the Jedi Order's ranks were increasingly thinned as the Republic grew weaker and public opinion turned against them.
After the Jedi discovered Sidious's existence thanks to a mecho-chair Nute Gunray accidentally left behind on Cato Nemodia and launched a hunt for him, the Sith Master decided the time had come to initiate his endgame. Sidious had General Grievous invade Coruscant and capture his alter ego. Anakin Skywalker and Obi-Wan Kenobi, who were fighting on the front lines, rushed back to Coruscant to rescue the Chancellor. During the skirmish, Dooku was killed by Anakin, and Grievous, who escaped, became the Confederacy's new leader. Afterwards, Sidious ordered Grevious to move the Separatist Council to Mustafar and, as Palpatine, informed Anakin that the cyborg was on Utapau. The Jedi High Council dispatched Obi-Wan to deal with him. The battle ended with Grievous's death at the hands of Obi-Wan, and Nute Gunray became the Confederacy's final leader. Unfortunately, Grievous was meant to lure Obi-Wan away so he couldn't stop Sidious from converting Anakin into his third and final apprentice, Darth Vader. After Vader's conversion and the Activation of Clone Protocal 66, Vader was dispatched to Mustafar and slayed the entire Separatist Council. Afterwards, Vader sent a deactivation signal to the entire droid army, shutting it down and ending the Clone Wars. Afterwards, Sidious, as Palpatine, proclaimed the birth of the Galactic Empire with himself as Emperor.