During the Clone Wars, the Jedi Order mounted a mission to rescue Jedi Master Quinlan Vos, who had been captured while on an assignment to assassinate Count Dooku.
After Asajj Ventress's failed attempt to rescue and sway Quinlan Vos from the dark side on Serenno, she escaped and met with Jedi Master Obi-Wan Kenobi in a bar on Coruscant. A month later, Ventress ran into the Mahran Jedi Knight Akar-Deshu. While his approach was met with hostility and reluctance to speak, he explained to him that Kenobi informed the Jedi High Council of what happened to Vos. Afterwards, he accompanied and presented her to the Jedi Council.
As Ventress entered the Jedi Council Chamber, Mace Windu greeted her with an arrest warrant, but Masters Kenobi and Yoda gave her the chance to provide information of Quinlan Vos. As she explained, initially, the Council members —particularly Mace Windu - interrogated her with tones of suspicion and hostility. Ventress answered truthfully— that she trained Quinlan Vos in the ways of the dark side, believing it was the best method to gather their strength to assassinate Dooku, which shocked the Council members. But Ventress made a point of reminding the Jedi Council that they were the ones who wanted to pair up Quinlan Vos and her to assassinate Dooku.
As she, Desh, and Anakin Skywalker left the Council Chambers, the Council debated on this new information. Kenobi believed that there was still a chance at saving Vos from the dark side, though this was met with mixed responses from the Council members. All of a sudden, Admiral Wullf Yularen contacted the Jedi Council regarding intel of Count Dooku and his new "Admiral Enigma": that Dooku's Providence-class Dreadnought was sighted above and ready to attack the planet of Taris. Yoda then presented Ventress with a deal—if she helped Kenobi and Skywalker bring back Vos to the Jedi Temple, then she would be given a full pardon of her war crimes.
Skywalker, Kenobi and Ventress boarded the Banshee, and she flew it into the hangar of Dooku's capital ship that was leading the fleet. The bounty hunter used Separatist codes to disable the hangar shields and enter the hangar. As they safely landed, they deduced that this "Admiral Enigma"—Vos—was on the bridge of the destroyer.
Ventress guided the two Jedi through the halls of the destroyer, avoiding battle droid patrols. Once they reached the bridge, the figure that rose from the captain's chair wasn't Vos - it was Dooku. With his red blade ignited, Anakin wasted no time in leaping to Dooku with his own blue lightsaber.
While Skywalker and Dooku dueled, the several battle droids on the bridge opened fire on Ventress and Kenobi. As Ventress accessed the computer on the lowest level of the bridge, Kenobi covered her by deflecting the incoming blaster fire with his own lightsaber. Ventress also used the Force to throw two battle droids together; this distracted Dooku. He fled down to the second level with Skywalker in close pursuit.
The duel between Anakin and Dooku seemed to be a stalemate. The Sith Lord released a blast of blue Force lightning at his opponent. Skywalker raised his blade to shield himself from the lightning. With his other hand, Dooku used the Force to throw parts of a destroyed battle droid at Anakin. He dodged by jumping to the third level below, with Dooku in pursuit.
More droids entered the bridge, opening fire on Ventress and Obi-Wan. While they were redirecting the blaster fire, Kenobi accessed the ship's computer and found out that Quinlan Vos was being imprisoned in the ship's brig below and that "Admiral Enigma" never existed. He concluded that Dooku had been using Vos as a tool to lower Jedi morale. As Ventress and Kenobi fled the bridge to the brig, Anakin still continued fighting Dooku.
Upon entering Vos' cell in the brig, Ventress and Kenobi discovered an emaciated and battered Vos hanging suspended from the ceiling with glowing shackles. In order to perpetuate the deception that Vos was a prisoner, Dooku had whipped him. Vos appeared glad to see both his former lover Ventress and his fellow Jedi Master Kenobi. As the two freed Vos from his restraints, Ventress saw his eyes flash and realized that he had embraced the dark side of the Force. However, Kenobi disbelieved Ventress and Vos claimed that he was still loyal to the light side and Ventress.
Asajj attempted to strike down Vos with her lightsaber, but was restrained by Kenobi. Before a fight could break out, battle droids arrived in the brig and the trio were forced to flee. Shortly later, they were rejoined by Skywalker, who used his lightsaber to slice a circular hole through the ceiling, crushing the battle droids below in the process. After making their way back to the hangar, the four boarded Ventress' ship, Banshee, and fled into space. While Kenobi and Skywalker were relieved to have rescued Vos, Ventress insisted that Vos could not be trusted. After evading vulture droids, the four escaped on the Banshee into hyperspace.
Despite rescuing Quinlan Vos, the Jedi mission actually played into the hands of the Separatists. In Dooku's captivity, Vos had already embraced the dark side and become the Sith Lord's apprentice. In secret, Vos planned to use his apprenticeship to Dooku to force the Sith Lord to lead him to Darth Sidious and thus allow him to destroy the Sith. Using his position within the Jedi Order, Vos leaked classified information about at least two Republic military operations to the Separatists. After Yoda discovered that Vos had indeed embraced the dark side, the Jedi Council concocted a mission for Vos to kill Dooku. If he failed the test, they would arrest him for treason. Meanwhile, Vos managed to reconcile with Ventress and reaffirmed his vow to marry her once he had killed Dooku.
As expected, Vos failed to carry out the mission, and he, along with Dooku, was promptly arrested by Kenobi and Skywalker. However, Vos managed to break out of his restraints and free Dooku. During the escape attempt, he killed two of his Jedi colleagues, Akar-Deshu and Kav Bayons. Together with Ventress, Vos and Dooku escaped aboard the Banshee and crash-landed on Christophsis. After trudging their way to the Separatist base there, Dooku contacted Darth Sidious for help in getting offworld. Vos only caught a fleeting glimpse of the mysterious Sith Lord. Shortly later, the Jedi and Republic attacked the Separatist base.
During the battle, Ventress was seemingly killed when she took the brunt of Dooku's Force lightning in order to protect her lover Vos. Dooku then tried to goad Vos into killing him, but the Jedi Master refused to take the bait and returned to the light side. While the Jedi secured the base and took Vos into custody, Dooku managed to escape with the help of Sidious. Since the mission to kill Dooku had brought Vos dangerously close to the dark side, the Jedi abandoned any future attempts to assassinate Dooku.