Deep within the mighty spires of Geonosis, Dooku chaired a meeting of the minds to formally create the Confederacy of Independent Systems. Separatist Senators alongside representatives from the Commerce Guild, the Trade Federation, the Corporate Alliance, the InterGalactic Banking Clan and the Techno Union pooled their resources together to form the largest military force in the galaxy. The Separatists were ready for war.
The Jedi Knight Obi-Wan Kenobi discovered the treasonous meeting and warned the Republic, but not without being captured. Kenobi was soon joined by Anakin and Padmé, who had come to Geonosis in an attempt to rescue him. Learning the presence of his master's son, Dooku released Anakin before he entered in the execution arena and bring him before him. Anakin explained his new plan to Dooku. Though uncertain about this, Dooku accepted, understanding that Anakin's plan was also concerning Kenobi's fate.
Two years later, at the formation of the New Order, Dooku and Anakin went in the Jedi Temple with troopers to arrest the Jedi Knights and consequently kill them. Unfortunately, as they were chasing some fugitives, Dooku was taken by surprise by three Jedi who killed him.