At some point during the Clone Wars, Dooku ordered the kidnapping of Jabba the Hutt's son Rotta on planet Tatooine carried out by his assassin Asajj Ventress and Ziro the Hutt, Jabba's uncle, in an attempt to frame the jedi and forge an alliance with the hutts. The attempt was successful and Dooku arrived on Tatooine to lie to Jabba about the jedi kidnapping his son. However, Anakin, now a jedi knight with a cybernatic right arm, and his padwan, Ahsoka Tano, were able to rescue Rotta and escape Teth while Obi-Wan stayed behind and defeated Ventress. Dooku was later informed that Anakin and Ahsoka were heading for Tatooine with Rotta and ordered his magnaguards to shoot their ship down. After they successfully shot down their ship, Dooku left to confront Anakin while his magnaguards fought Ahsoka. When Dooku found Anakin, he ordered the hero to surrender Rotta to him or die, but Anakin revealed Rotta was with Ahsoka, sparking a duel between the two. During the fight, Dooku revealed to Anakin about Ahsoka's conflict with the magnaguards. In response, Anakin knocked Dooku onto the sand and stole his speeder bike to save Ahsoka. After destroying the droids, Anakin and Ahsoka returned Rotta to Jabba and told the truth about Dooku and Jabba allied with the Republic as thanks, foiling Dooku's scheme. However, Dooku had escaped from Tatooine while Anakin returned Rotta to his father and Ziro was arrested. Later, Dooku sent Ventress to Toydaria in hopes of allying King Kantuunko with the Separatists. When Kantuunko decided to join the Republic, Dooku ordered Ventress to kill the king, but was foiled by Yoda, and Ventress escaped Toydaria. Later, Dooku assisted his cyborg right hand servant General Grievous on board his warship the Malevolence, which possessed a powerful ion cannon that could destroy entire Republic fleets . As time went by, Grievous destroyed many Republic fleets and many warships, most notably the Triumphant during the battle of Abregado which had impressed Dooku. Later, Dooku ordered Grievous to attack a Republic medical station in the Kaliida Nebula. Grievous attacked, but during the battle, the ion cannon was badly damaged just as Republic reinforcements arrived to destroy the Malevolence. Dooku informed Grievous via hologram that Senator Amidala was heading for the sector and if Grievous could capture her, the clones would have to retreat, giving enough time for the Malevolence to escape. Grievous captured the senator, but a jedi invasion forced Grievous to flee. The Malevolence was destroyed when it crashed into a nearby moon, but Grievous escaped in his starfighter, and Amidala was rescued by Anakin, much to Dooku's frustration. Later, Dooku was informed of Viceroy Nute Gunray's capture on the planet Rodia. In response, Dooku sent Ventress to attack the Tranquility, which was the ship Gunray was incarcerated on and was heading to Coruscant, and rescue Gunray. When Ventress and a group of battle droids infiltrated the Tranquility and fought the jedi Luminara Unduli and Anakin's padwan Ahsoka Tano on board the ship, Dooku sent a signal to senate commando Faro Argyus, whom he bribed, to liberate Gunray. Ventress was able to evade the jedi and escaped with Gunray and Argyus. After their escape, Argyus was killed by Ventress when he tried to discredit her. Later, Dooku contacted Grievous, demanding more dead jedi and clones. To set up a test for his second-in-command, Dooku used a Republic tracking beacon to trick the jedi into thinking Gunray was on the third moon of Vassek and lur them into Grievous's fortress. Jedi Kit Fisto and Nadhar Vebb intercepted the signal and headed for Vassek with a small group of clones and made their way into the fortress. When they figured out Gunray wasn't there, Dooku appeared to the search team via hologram and offered them an "alternative prize". Later, Dooku contacted Grievous again and Grievous informed him that he killed all the clones and Vebb, but Fisto defeated him and escaped to Coruscant, to which Dooku replied that there was "room for improvement". Later, the Republic tracked Dooku down and Anakin and Obi-Wan infiltrated his frigate and cornered him as Republic troops arrived, but Dooku fell through an escape hatch before Anakin could capture him. Anakin went after him through the hatch, but Dooku delayed him with his force lightning. When Dooku reached the hangar, he boarded his solar sailer and escaped, but was pursued by Anakin and Obi-Wan using a stolen Separatist ship. The jedi opened fire on the Count and shot Dooku down, forcing him to crashland on the planet Vanqor. Dooku attached a tracking beacon to his ship and escaped into the caves just as Anakin and Obi-Wan landed on the surface to capture him. Anakin destroyed the beacon and went with Obi-Wan into the caves. Dooku caused a cave-in with the force that trapped the jedi and stole Anakin's lightsaber. After escaping the caves, Dooku came across a gang of Weequay pirates led by Hondo Ohnaka. Dooku asked Hondo to take him to a civilized planet. Hondo and his gang took Dooku with them to their headquarters on the planet Florrum. Upon arrival, the pirates captured Dooku and disarmed him. Later, Hondo contacted Chancellor Palpatine and informed him of Dooku's capture and was holding him for ransom. He offered 1,000,000 credits in spice in exchange for Dooku. Palpatine sent Anakin and Obi-Wan to Florrum to confirm Dooku was indeed being held by the pirates. They found Dooku in a holding cell who warned them not to trust the pirates, but they did not listen and were captured by the pirates who were wanting to triple their pay. Meanhile, Senator Kharrus, Representative Jar Jar Binks, and a group of clones led by commander Stone arrived in Florrum to pay the pirates. Dooku, Anakin, and Obi-Wan escaped three times, but were recaptured and imprisoned. Later, Anakin and Obi-Wan were taken to Hondo for electrical torture. Later, during a power outage caused by Jar Jar crashing a tank into a power field, Dooku killed the pirate guarding his cell and escaped. After retrieving his lightsaber, Dooku made his way to the hangar and force choked Hondo's second-in-command, Turk Falso, to death, but not before forcing him to kill his partner Barb Mentir with his blaster. Dooku then stole their ship and ultimately escaped Florrum as Anakin and Obi-Wan were rescued by Jar Jar and Stone. Later, Dooku gave general Lok Durd permission to construct the weapon called the Defoliator. Durd demonstrated the Defoliator's capabilities: it could incinerate organic life and leave battle droids unharmed. Dooku was impressed when the first test was successful, but knew Durd only created the Defoliator to get a promotion. Dooku then instructed Durd to use the Defoliator on the Lurmen inhabitants of the isolated planet Maridun, so they could see how the Defoliator effected living creatures. Unfortunately, the attempt failed as a small group of clones and jedi defended the Lurmen and Anakin destroyed the Defoliator and captured Durd. Later, Separatist leader Wat Tambor invaded and successfully took control of the planet Ryloth. Dooku gave Tambor strict orders to prevent the Republic from interfering with their control. However, the Republic arrived and broke through the Separatist blockade and proceeded to deploy clones and jedi to the surface to liberate Ryloth from Tambor's control. Dooku ordered Tambor to steal every valuable resource from the capital city Lessu and escape Ryloth before the Republic arrives. TA-175, Tambor's tactical droid, kept in contact with Dooku against Tambor's orders. Later, clone troopers led by jedi general Mace Windu and the Twi'lek freedom fighters led by Cham Syndulla attacked Lessu to capture Tambor. However, unknown to Tambor, Dooku planned to bomb Lessu whether Tambor had fled or not and TA-175 betrayed Tambor and fled in Tambor's vessel, leaving Tambor behind to be captured by Windu. Meanwhile, Dooku's plan to bomb Lessu ultimately failed as Anakin and Ahsoka shot down the bombers before they could drop the bombs. Later, Dooku forged an alliance with a Mandalorian terrorist organization known as Death Watch, led by Pre Vizsla, whose goal was to take over the planet Mandalore and defeat the pacifist government called the New Mandalorians, led by Duchess Satine Kryze. Dooku urged Vizsla to give the Republic a reason to send military prescence to Mandalore, which Dooku believed would inspire revolution. However, despite multiple assassination attempts, Satine proved her case to the senate and caused them to call off the occupation of Mandalore, despite the actions of an assassin sent by Dooku and Vizsla to kill her. When a frustrated Vizsla promised to attack Mandalore, Dooku told him to hold off his attack as he would likely end up ruling Mandalore for one day and that there were other ways to accomplish Death Watch's goal to conquer Mandalore. Later, the Galactic Senate refused to de-regulate the banks and Techno Union officials contacted Dooku, suggsting he bring the war to Coruscant's doorstep. In response, Dooku ordered Grievous to snd Demolition droids undercover to Coruscant to sabotage the capital. Meanwhile, on planet Raxus, Dooku publicly supported a peace treaty between the Republic and the Separatists. However, Dooku still planned to prolong the war. Grievous's successful sabotage of Coruscant prolonged Dooku's plans. After the attack, Dooku was informed that senator Mina Bonteri had been responsible for the peace treaty and ordered his agents to kill her, and Dooku later contacted the Republic and lied to them about a Republic attack on Raxus to cover up Bonteri's death, but was blown by spies. Later, Dooku hired two bounty hunters, Robonino and Chata Hyoki, to kill any senators voting against their new bill. The duo managed to injure or kill twenty senators, but were arrested after an attempt on Amidala and Bail Organa's lives and the bill was vetoed. Later, in his lair on planet Serreno, he was informed of Ventress's growing power and Dooku decided to eliminate her. He ordered his droids to destroy their command ship, where Ventress was fighting Anakin and Obi-Wan. Anakin and Obi-Wan escaped while Ventress was seemingly killed. Unknown to Dooku, Ventress survived and escaped to planet Dathomir where she enlisted aid from the Nightsisters. Later, Ventress and two nightsisters turned invisible and used jedi lightsabers to attempt to assassinate Dooku, who fought them. Dooku eventually defeated the Nightsisters and used force lightning to send them off a cliff, which they survived. Dooku believed the jedi were responsible for the attack and contacted Mother Talzin who informed him that she would find a replacement for Ventress. Later, Dooku traveled to Dathomir to discuss with Talzin. She mentioned Darth Maul, who Dooku knew had died on Naboo at the hands of Obi-Wan. Later, the Nightsisters presented a Nightbrother with enhanced dark force abilities named Savage Opress to Dooku and he took Opress to Serreno to be his new apprentice. On Serreno, Dooku gave Opress his first task: attack a sancuary on planet Devaron, which he carried out successfully. After informing Dooku of his success, Dooku congratulated him and promised one day they will rule the galaxy together. After training, Dooku sent Opress to Toydaria to capture King Kantuunko. Despite resistance from Anakin and Obi-Wan, Opress successfully captured the king, but killed him in an escape attempt. When Opress returned to Dooku with the deceased king, Dooku shocked Opress with lightning, angering Opress and resulted in a fight. During the battle, Ventress revealed herself to Dooku much to his surprise and sided with Opress against Dooku. Despite his best efforts, Opress was no match for Dooku's force lightning. Ventress angrily ordered Opress to continue, but refused and attacked Ventress, giving Dooku time to flee. He soon confronted Ventress again, but she failed to defeat him and escaped in an escape pod, but not before blinding Dooku for the time being. Later, Dooku was informed of jedi general Even Piell's capture and imprisonment in a Separatist prison called the Citadel on the planet Lola Sayu and figured out he had information on the Nexus Routes which could change the tide of the war. Because of this, Dooku pressured the sadistic warden of the Citadel and Separatist operative, Osi Sobeck, to interrogate Piell and his men about the Nexus Routes. Later, a group of jedi and clones led by Anakin, Ahsoka, and Obi-Wan infiltrated the Citadel frozen in carbonite, but their cover was blown when one of the clones accidentally triggered an electro-mine and was killed. Despite his best efforts, the jedi evaded Sobeck's traps and successfully rescued Piell and his head naval officer Wilhuff Tarkin and many others. Dooku was furious and contacted Sobeck and ordered him to recapture Piell and his naval officers and capture the rescue squad, but Sobeck assured him that everything was under control and ended transmission and proceeded to prevent the jedi from escaping with Piell by destroying a Separatist ship and killed a clone named Echo, ho sacrificed himself to destroy the droids, but the jedi and the surviving clones and naval officers fled to the caves below to contact the Republic for assistance. At the same time, Dooku attempted to contact Sobeck again, but Sobeck ignored him to cut off the jedi's escape. Eventually, Dooku was able to contact Sobeck, who informed the warden of the significance of the jedi's capture, to which Sobeck swore to accomplish, but Dooku reminded him that Sobeck's promises to capture the jedi were the only things that were keeping him alive. Although Sobeck sent Anoobas to track the jedi and successfully killed Piell, Sobck ultimately failed to stop the jedi from escaping the Citadel with the Nexus Route information and was killed by Ahsoka and the jedi, clones, and the naval officers escaped. Later, Dooku sent Separatist operative Riff Tamson to assassinate Yos Kolina, the king of planet Dac, to disrupt tensions between the planet's two native species: the Mon Calamari and the Quarren, which Tamson carried out successfully and relations between the two races declined and the Quarren allied with the Separatists, while the Republic backed the Mon Calamari and sent an army of clones and jedi to quell the tensions, but Tamson attacked the Mon Calamari on Dooku's orders and attempted to kill Prince Lee-Char, son of the deceased Yos Kolina, but the Republic forces drove him back and retreated. Dooku contacted Tamson and ordered him to unleash the Hydroid Medusas on the Mon Calamari, which he did succssfully and captured many Mon Calamari and clones and killed several others. After this, Dooku contacted Tamson and ordered him to kill Lee-Char. However, the Republic destroyed the Separatist signal tower and sent a distress signal to Naboo and the Gungan army came to their aid, but Tamson was able to capture the jedi and a majority of Gungans, but Lee-Char was able to elude him with Ahsoka. Later, When Dooku contacted Tamson and Nossor Ri, Ri questioned the outcome of the defeat of the Mon Calamari, but Dooku responded that Tamson had sent his own troops to help. However, Lee-Char was able to liberate his people and the clones and jedi freed themselves and Lee-Char convinced the Quarren are only being used by the Separatists to further their goals. Lee-Char then confronted Tamson himself and threw an explosive knife at Tamson, killing him and foiling the Separatists once again. Later, Dooku traveled to Naboo. While there, he ordered his agent Minister Rish Loo to hypnotize the leader of the Gungans, Boss Lyonie, to rallying the gungans against Naboo, but was foiled by Anakin and Lyoni wwas knocked out while Rish escaped. Later, representative Jar Jar Binks disguised as Lyonie put the attack on Theed, Naboo's capital, on hold and Rish escaped on a speeder bike pursued by Anakin. Later, Dooku was informed of Grievous's capture and planned a trap for Anakin and contacted Rish to lure Anakin to his location. When Rish lead Anakin to Dooku, Dooku killed Rish and fought Anakin. During the fight, Dooku activated MagnaGuards to help him. Anakin destroyed the Magnaguards, but Dooku defeated the hero and captured him. He later contacted Amidala and told her if she would release Grievous, he would return Anakin in exchange. Amidala accepted the Count's request and released Grievous and in turn, Dooku released Anakin and the Separatists left Naboo. Later, Dooku met up with the Zygerrian race, who were allied with the Separatists from the beginning and were seeking to rebuild their slave empire after it was destroyed by the jedi years before the war. Later, Dooku and the Zygerrians traveled to planet Kiros and made an agreement with the Togrutan colonists to protect them for the rest of the war, and Dooku promised the colonists a "temporary safe haven" until the war had ended. The Separatists then proceeded to abduct all of the colonists and board them on Zygerrian slave ships which carried the colonists to slavery on the planet Zygerria where the Zygerrian queen Miraj Scintel was planning a royal slave auction. Dooku left a Zygerrian slaver and Separatist operative Darts D'Nar in charge of his droids on Kiros. D'Nar proceeded to plant bombs across the village and linked the final two together so one would go off if the other was tampered with. Later, Republic forces arrived to rescue the colonists to no avail, but they easily defeated most of D'Nar's droids, prompting him to contact Obi-Wan to agree on terms of surrender. While negotiating surrender with Obi-Wan, Dooku ordered D'Nar to kill Obi-Wan and ended transmission. Obi, Wan narrowly subdued D'Nar while Anakin and Ahsoka disabled the bombs. D'Nar then proceeded to flee in his ship to Zygerria, but one of the ship's engines was disabled by Anakin and Anakin and Ahsoka captured D'Nar and forced him to reveal the location of the colonists. Later, Dooku was informed that Anakin, Obi-Wan, and clone commander Rex infiltrated Zygerria disguised as Zygerrian slavers and Ahsoka was disguised as a slave. Anakin kept Scintel occupied while Rx and Obi-Wan attemptd to free the colonists, but were captured. Ahsoka was captured as well, but Scintel kept Anakin as her servant while Obi-Wan, Rex, and the colonists were relocated to planet Kadavo. After being informed of this, Dooku traveled to Zygerria to speak with Scintel. Once there, Scintel told Dooku that she kept Anakin alive because she believed him to be a valuable servant and revealed that Obi-Wan would soon realize that he could no longer help the colonists and cause his spirit to sink into servitude and told Dooku about the advantage of having an army of enslaved jedi at his commannd. However, Dooku revealed to the queen that he has no desire to enslave jedi, but execute them and ordered her to summon Anakin and kill him, but she refused and Prime Minister Antai Motec betrayed her and Dooku force choked her before Anakin intervened using a shock whip, but was no match for Dooku and escaped from the palace with a dying Scintel to regroup with a freed Ahsoka. Later, Dooku contacted keeper Arguss stationed on Kadavo and ordered the execution of Obi-Wan and ended transmission just as Anakin, Ahsoka, and Republic reinforcements arrived. During the battle, Dooku's plans to enslave the colonists failed and the colonists were freed by Ahsoka and Rex killed Arguss and Anakin and Obi-Wan and the rest of the Republic escaped just as the facility exploded. Later, Dooku told Separatist operative and criminal mastermind Moralo Eval to orchestrate a plan to kidnap and kill Chancellor Palpatine on Coruscant. During the plan, Eval hired the bounty hunter Cad Bane to help him carry out his plan. Eventually, Republic forces tracked down and captured Eval and incarcerated him, but Palpatine and the Republic believed that the attempt on his life was still in effect. Bane was also incarcerated some time later. In response, the jedi council had Obi-Wan disguised as the assassin Rako Hardeen to infiltrate the prison where Eval was being held in hopes of getting information on Eval's plans. After gaining their trust, Obi-Wan, Bane, and Eval escaped from prison and fled to Nal Hutta, where they acquired a ship and new weapons and contacted Dooku, who was frustrated that Eval was late to the meeting on Serreno. Eval told Dooku he would be running late and ended transmission. Eventually, Eval, Bane, and Obi-Wan escaped Nal Hutta and were briefly pursued by Anakin and Ahsoka, who were unaware of Obi-Wan's undercover mission, but the trio lost them. After landing on Serrano, Dooku greeted the trio and ordered Eval to prepare the box, a training facility Eval invented to test a group of eleven bounty hunters to kidnap and assassinate Palpatine. As the tests went on, Dooku questioned Eval about Hardeen and was growing suspicious, to which he replied that he "killed" Obi-Wan. In the end, Bane, Obi-Wan, and three other bounty hunters survived and Dooku selected Bane as the leader of the bounty hunters. The next day, Dooku briefed the bounty hunters on their mission and gave them holographic devices to disguise themselves as senate commandos. After the briefing, Dooku, who was still suspicious about Hardeen, suggested he keep a close eye on him, which the bounty hunter agreed to do. Obi-Wan was given orders to snipe the chancellor. Later, Palpatine arrived on Naboo for the ceremony of light. After Obi-Wan gave the signal to Windu to alert him of the bounty hunter's prescence, Bane and his men attacked and Obi-Wan began assisting Windu and Anakin by sniping the bounty hunters, but Bane and Eval succeeded in taking Palpatine hostage and fled in a speeder heading for the rendevouz point where Dooku would meet them, though Obi-Wan pursued in a speeder. Upon arrival, Bane and Eval noticed Dooku was absent. Instead, Dooku took advantage of the chaos and slipped a comlink in Obi-Wan's sniper blaster's case to listen in on Obi-Wan and eventually discovered that Rako Hardeen was Obi-Wan in disguise. Meanwhile, Obi-Wan revealed himself to Bane and Eval and rescued Palpatine, leaving the infuriated duo to be arrested by Windu and Anakin. After the failed attempt on Palpatine's life, Dooku awaited Palpatine and Anakin in the palace's dining room accompanied by two magnaguards, which shocked the jedi and the chancellor. Anakin ordered Palpatine to run, which he did, but a third magnaguard blocked the entrance to the dining room, preventing the chancellor's escape and Dooku fought Anakin. Eventually, Anakin destroyed the magnaguards and drove Dooku into the corridor, where Anakin slowly gained the upper hand, but Dooku used his force lightning to shock Anakin for the time being, but Obi-Wan(still disguised as Rako Hardeen), intervened to help Anakin. Anakin, with Obi-Wan's help, successfully overpowered and defeated Dooku, but Dooku hopped aboard his waiting Solar Sailer and ultimately escaped Naboo.