During the Clone Wars, Asajj Ventress sought the assistance of Krayt's Claw, a bounty hunter syndicate headed by Boba Fett. She hired them for a mission: to extract Jedi Master Quinlan Vos from Castle Serenno on Serenno. Unbeknownst to Ventress, Count Dooku had already corrupted Vos to the dark side by revealing Ventress' role in the death of his Master Tholme. Consequently, Vos rejected Ventress' rescue attempt and instead turned against her. Ventress and her bounty hunter allies were then compelled to escape, leaving Vos behind to become Dooku's new Sith apprentice.
The Jedi High Council made the decision to assassinate Sith Lord Count Dooku, the leader of the Separatists, following his massacre of civilians on Mahranee. Their goal was to bring an end to the Clone Wars. Quinlan Vos, a Jedi Master known for his skills in undercover operations, was chosen for this dangerous task. Vos then enlisted the help of Asajj Ventress, a Nightsister who was formerly Dooku's Sith apprentice. Ventress, seeking vengeance against Dooku, agreed to assist and subjected Vos to rigorous training to enhance his dark side powers.
Later, Ventress and Vos learned that Dooku was traveling to Raxus Secundus, a Separatist world located in the Tion Hegemony, to accept the Raxian Humanitarian Award at a public event. The two Force-users successfully infiltrated the ceremony and engaged the Sith Lord in combat at a secluded overlook. Despite their preparations, they were unable to overcome Dooku's dark side mastery. When General Grievous and Separatist droid forces arrived to aid Dooku, Ventress was compelled to flee. Ultimately, Vos was captured, rendered unconscious with Force lightning, and taken to Castle Serenno on Serenno.
While imprisoned by Dooku, Quinlan endured extended periods of torture. After resisting for some time, Vos finally succumbed to the dark side after Dooku revealed that Ventress had murdered his late Master Tholme. Dooku thus succeeded in turning Vos against his former lover. Meanwhile, on Tatooine, Ventress visited Chalmun's Spaceport Cantina where she encountered bounty hunter Boba Fett and his syndicate, Krayt's Claw, which included bounty hunters Bossk, Latts Razzi, Embo, and C-21 Highsinger. Ventress hired the bounty hunters to rescue Vos, offering them 250,000 credits, representing her entire accumulated wealth from her bounty hunting career.
Ventress, accompanied by Krayt's Claw, journeyed to Serenno aboard the Slave I and Embo's saucer-shaped starship, the Guillotine. Ventress then initiated her plan. While the bounty hunters created a distraction, Ventress would infiltrate Dooku's palace and proceed to the prison. Following some discussion, the bounty hunters decided to steal a starship. Under Fett's command, the bounty hunters attacked two disembarking ships and their battle droid escorts. Embo decapitated two droids using a disk-shaped metal weapon, while Latts employed a grappling boa to ensnare another droid. Highsinger then crushed it with his metallic feet.

As the bounty hunters exchanged fire with battle droid reinforcements, Ventress infiltrated Dooku's prison. Inside the prison complex, she discovered that almost all the cells were empty. While navigating the prison, she used her lightsaber to eliminate several droid sentries, including two wielding battle staves. After destroying the droid sentries, Ventress finally located Vos' cell. However, Vos, grieving over the murder of his Master Tholme, was consumed by rage at Ventress' presence and used the Force to choke her, accusing her of being a liar and a murderer.
Ventress attempted to reason with her former lover, but Vos violently threw her against the dungeon's stone floor. During the attack, Asajj noticed that Quinlan's eyes had turned a blood-rimmed shade of yellow, indicating his fall to the dark side. Overwhelmed by rage, hatred, and the influence of the dark side, Vos ignited Tholme's lightsaber and attacked Ventress. She was then forced to activate her own lightsaber in self-defense. As they fought, Vos accused her of using him, while Ventress tried to reason with him, explaining that the dark side was clouding his mind. Ventress also suggested that Vos abandon Dooku and the Jedi Order.
Unable to reason with Vos, Ventress was forced to flee the prison. Quinlan pursued her, using the Force to hurl broken pieces of battle droids at her. Eventually, Asajj managed to escape the prison, where she was met by Boba Fett and his companions, who had trapped Dooku under some webbing. With Vos determined to kill Ventress and anyone who stood in his way, she and her bounty hunter allies were compelled to flee Serenno without him. As Ventress departed aboard a stolen shuttle, she witnessed Vos and Dooku walking together, confirming that Vos had become Dooku's newest Sith apprentice.
Following the unsuccessful rescue attempt, Asajj Ventress traveled to Coruscant and informed Quinlan's friend, Master Obi-Wan Kenobi, that he had joined Count Dooku. Over the following months, Vos assumed his role as Dooku's new right-hand man, earning the title "Admiral Enigma" in HoloNet news reports. At some point, Ventress encountered Vos' friend, the Jedi Knight Akar-Deshu ("Desh"), who informed her that the Jedi were debating whether or not to rescue Vos. At Kenobi's request, Desh invited Ventress to help persuade the Jedi Council to support their plan to rescue Vos.
At the Jedi Council Chambers, Ventress was met with hostility by some of the Jedi Masters, but Masters Kenobi and Yoda vouched for her. During the meeting, Ventress admitted that she had trained Vos in the ways of the dark side, believing that it was the best way to accomplish the mission to kill Dooku. When some of the Jedi criticized her, Ventress responded by reminding the Council that they were the ones who had paired her with Vos in the first place. After further deliberation, the Jedi Council agreed to launch a mission to rescue Vos. They also reluctantly agreed to allow Ventress to participate in the mission in return for pardoning her of all crimes against the Republic and the Jedi. The Council's decision to proceed with the rescue mission was strengthened by an intelligence report from Admiral Wullf Yularen that Dooku and Admiral Enigma were planning to attack Taris.
With Ventress' assistance, Master Kenobi and his former apprentice Anakin Skywalker successfully infiltrated Dooku's Providence-class Dreadnought. Together, they reached the bridge where they confronted Dooku and quickly realized that "Admiral Enigma" was a pseudonym. They also managed to reach the ship's brig and locate Vos. While Vos appeared to be emaciated and brutalized, Ventress quickly sensed that it was a deception and that her former lover had succumbed to the dark side. Despite her protests, Vos was welcomed back into the Jedi Order. However, he used his position to advance the Separatist cause. In secret, Vos planned to use his loyalty to Dooku to learn the identity of his mysterious master Darth Sidious and destroy the Sith once and for all.