- "Haha! Surely no one can stop the CIS! And it's all thanks to me and my strong, sturdy, immovable head."
- ―Count Dookie, shortly before having his head cut off
The Confederacy of Independent Systems, also known as the CIS, Cresh-Isk-Senth, or Separatist Confederacy, was a government and separatist movement formed by planets and systems that wanted to secede from the Galactic Republic because they didn't want to pay taxes. And they wanted to maintain their systems' rights. And they thought the Galactic Senate was corrupt or something. The Confederacy fought against the Republic in the Clone Wars, and was doing okay until Darth Vader killed its leaders and turned off their droids, shutting down the Droid Army and Confederate Navy.
The Confederacy's formation was part of a scheme by Darth Sidious to create a war so he as Supreme Chancellor could be voted enough power to in the Galactic Senate to eventually exterminate the Jedi, declare himself emperor, and rule the galaxy.
- "NOOOO‼ How could I have lost a game of dejarik⁈ This is unfathomable!"
- ―Dooku loses a fateful game of dejarik to Sifo-Dyas.
The Confederacy of Independent Systems got its roots first started when Jedi Master Dooku lost a game of dejarik to Master Sifo-Dyas. Dooku was immensely upset because he had never lost a game of dejarik since becoming a Jedi Master.
Believing that the Jedi Order had not taught him to be the very best dejarik player, Dooku left the Order and re-assumed his noble title Count of Serenno. He also became a Sith Lord called Darth Tyranus, apprenticed to Darth Sidious, who was a dejarik grand master. Lord Sidious promised to teach Lord Tyranus to be an even better dejarik player, but for that to happen, Lord Tyranus had to go help with some convoluted galactic power-gaining scheme by Lord Sidious. So Count Dooku stirred up anti-Republican sentiment on many planets and in many star systems, and preached secession. These planets formed the Confederacy of Independent Systems as a common government with Count Dooku as its head of state. The Commerce Guild, Corporate Alliance, InterGalactic Banking Clan, Techno Union, and Trade Federation joined the Confederacy along with the independent systems.
The Trade Federation and other aforementioned groups secretly churned out billions of cheap budget value battle droids from foundries to add to their existing droid armies, combining them to form the Separatist Droid Army. Their fleets and those of the separatist systems were combined to form the Confederate Navy. The separatists planned to use these forces to force the Republic to meet their demands and recognize the Confederacy's independence.
Jedi Master Obi-Wan Kenobi discovered Count Dooku and the Confederate plans on Geonosis, but he got captured. Anakin Skywalker and his woman Padmé Amidala came to rescue him, but they failed and got captured. A Jedi force came to rescue them, but the battle droids started killing them. Master Yoda came to rescue them with an army of Jango Fett clones conveniently created for the Republic on Kamino that no one in the Galactic Senate knew about: the Grand Army of the Republic. The clones fought the droids and won, Count Dooku cut off Anakin's arm and ran away, Jango Fett, himself in the employ of the CIS, got his head cut off by Mace Windu, and begun the Clone Wars had.
The Confederacy of Independent Systems and the Galactic Republic fought for three years. The Confederacy did well at first and won many battles. Count Dooku recruited force-sensitives like Asajj Ventress and Savage Opress as his Dark Acolytes to oppose the Jedi who were leading the Republican war campaigns. A wheezing Kaleesh cyborg warlord named Grievous became a Confederate general and Supreme Commander of the armies of the Confederacy because he had a grievance with the Republic and the Jedi or something. The Confederacy seemed to be winning the fight in the Outer Rim, but after a Republican offensive it began to lose the advantage.
After getting high on spice, Count Dooku decided that attacking Coruscant and kidnapping Supreme Chancellor Palpatine was a good idea. Sadly, this otherwise absolutely flawless plan ended in Palpy escaping, and Dooku getting his head cut off. Great job guys. Afterwards, General Kenobi killed General Grievous on Utapau. Then Darth Vader killed the separatist leaders on Mustafar and shut down all their droids, putting an end to the Clone Wars and the Confederacy of Independent Systems.
Although the Clone Wars were over, some people didn't seem to get the message. Some of those people on former separatist planets continued to fly the Confederate flag in acknowledgement of their history, but Imperial authorities often asked them to take it down. Others continued fighting as Separatist holdouts, and they too flew the Confederate flag.