Within the first decade of Supreme Chancellor Palpatine's rule, Count Dooku emerged as the face of the Separatist movement, rallying systems to his cause -- though some planets, such as the strategically located trade world of Eriadu, resisted his entreaties. On Geonosis, he conspired with other leaders to construct a massive droid army that would overwhelm the Republic. He was surprised to find, however, that Obi-Wan Kenobi had made his way to the system while on mission. Once the Jedi was captured, Dooku claimed he was glad to meet him -- as the former Master of Qui-Gon Jinn, Dooku had heard only good things about Obi-Wan -- and asked for his help. The reason Dooku joined the Separatists, he said, was that he learned a terrible truth: a Sith Lord called Darth Sidious controlled the Senate. With Obi-Wan at his side, they could destroy the Sith. “I’ll never join you, Dooku,” the Jedi said. Dooku coldly left Obi-Wan in his cell.

Later, Dooku and the Geonosians planned to execute Obi-Wan, as well as Anakin Skywalker and Padmé Amidala, in their massive arena. The three staved off the beasts unleashed upon them, however, which gave the Jedi and their new clone army time to stage an attack. Thus marked the start of the Clone Wars, with both sides suffering heavy losses.

In his bid to escape, Dooku rode a speeder to a nearby hangar but was followed by Obi-Wan and Anakin. The Separatist leader ignited a red-bladed lightsaber -- evidence that he had in fact turned Sith -- and struck Anakin with a powerful shot of Force lightning. Arrogant and eager for combat, he taunted them both, ultimately wounding Obi-Wan and severing Anakin’s right arm. Ready to finish the Jedi, Dooku stopped when he heard familiar footsteps: Yoda had arrived. The Sith claimed to be more powerful than any Jedi, but Yoda easily absorbed his Force lightning attack. “Much to learn you still have,” he said. With that, the two fought a furious lightsaber duel, which ended with Dooku making a hasty exit. “This is just the beginning,” he warned. The former Jedi fled the system and landed in an unmarked dwelling on Coruscant, greeted by the evil Darth Sidious. “I have good news for you, my lord,” he said. “War has begun.”

Dooku remained the face of the Separatist army, bringing war to planets across the galaxy. He also sought to undermine the Republic with a steady stream of propaganda sent over the information network known as the HoloNet, an effort that was opposed by Republic officers such as Wilhuff Tarkin. On numerous occasions throughout the Clone Wars, he dueled Anakin Skywalker and Obi-Wan Kenobi, and continually performed the will of Darth Sidious. During this time, Dooku took on an apprentice named Asajj Ventress. He trained her in the ways of the dark side and used her as an assassin; when Sidious deemed her value spent, Dooku abandoned her. Ventress, though, wanted revenge. Conspiring with Mother Talzin, they sent Savage Opress to be Dooku’s new apprentice; the real plan, however, was for Ventress and Opress to kill Dooku. This was not to be, as the Sith Lord was too strong with the dark side and survived the attack.

While Dooku was the leader of the Separatist movement, it was later revealed that his involvement in the origins of the Clone War stretched much deeper. With new evidence into the death of Sifo-Dyas -- the Jedi who supposedly ordered the creation of the clone army -- Obi-Wan Kenobi and Anakin Skywalker visited the Pyke Syndicate on Oba Diah. They learned that the Pykes were hired by a man named Tyranus to kill the Jedi, but that the crime family had secretly kept his companion, Silman, alive. Obi-Wan and Anakin began to speak to the captive, but he was quickly Force choked by an unseen attacker: Count Dooku had arrived, sent by Darth Sidious to tie up all loose ends to the death of Sifo-Dyas. Lom, leader of the Pykes, called Dooku by his Sith name -- revealing to the Jedi the unsettling truth behind the mystery of the clone army. Dooku, or Darth Tyranus, escaped, and the Jedi had no choice but to continue playing the Sith’s game.

In a daring move, General Grievous and Count Dooku abducted Supreme Chancellor Palpatine from Coruscant. In the resulting Battle of Coruscant, the clone army of the Republic and Separatist military forces clashed in the stratosphere of the city-planet. Through the heated battle, Anakin Skywalker and Obi-Wan Kenobi piloted their Jedi starfighters to Grievous’ flagship, hoping to rescue the Chancellor. Boarding the massive cruiser, they made their way to the ship’s tower and found Palpatine bound to a chair. Dooku appeared, engaging both Jedi at the same time. He first defeated Obi-Wan, Force choking him and nearly crushing the Jedi Master with a heavy railing. An enraged Anakin continued the fight, unleashing a strength Dooku had not anticipated. The young Jedi cut off the Sith Lord’s hands, drew Dooku’s lightsaber to him, and the Separatist leader fell to his knees. While Anakin debated what to do, Palpatine encouraged him to destroy Dooku. “Kill him now,” Palpatine commanded. Dooku looked to the Chancellor in disbelief, then to Anakin. His expression betrayed a new understanding of what had transpired, but it was a fleeting moment; Anakin decapitated Dooku with one swift motion.