The Confederacy of Independent Systems initiated a mission during the Clone Wars; its objective was to liberate Trade Federation Viceroy Nute Gunray. The Galactic Republic had previously captured him on Rodia. While Jedi Master Luminara Unduli, along with Padawan Ahsoka Tano, Clone Commander CC-1004 "Gree," and Senate Commando Captain Faro Argyus, were transporting Gunray back to Coruscant aboard the Venator-class Star Destroyer Tranquility, Asajj Ventress infiltrated the vessel. Subsequently, the ship came under attack from numerous vulture droids and boarding ships that deployed B2-series super battle droids. As Green Company faced the droid assault, Ventress detonated explosives, destroying the reactor room. After dueling and defeating Unduli and then evading Tano, she made her escape with Gunray and Argyus. Argyus had betrayed the Republic, incapacitating Gree to facilitate Gunray's freedom. However, Ventress executed Argyus as they fled in a stolen Consular-class cruiser.
Back in 22 BBY, Trade Federation Viceroy Nute Gunray found himself captured on Rodia by Senators Padmé Amidala and Onaconda Farr. He was held on the Tranquility, guarded by Jedi Master Luminara Unduli, Padawan Ahsoka Tano, Clone Commander CC-1004 "Gree," and Senate Commando Captain Faro Argyus, awaiting transport to Coruscant for his trial. Simultaneously, Darth Sidious charged his apprentice, Count Dooku, with the task of freeing Gunray. Dooku's plan involved dispatching the Dark Acolyte Asajj Ventress to divert the Jedi, while Argyus, handpicked for the mission by Chancellor Palpatine, would reveal his treachery to aid Gunray's escape. Sidious expressed doubt about Ventress's capabilities, but ultimately permitted Dooku to deploy her.
As the Jedi interrogated Gunray, a clone naval officer alerted them to the imminent arrival of a Separatist boarding party emerging from hyperspace. These ships unleashed B2-series super battle droids and B2-HA series super battle droids into the hangar bay. The Separatist forces swiftly overwhelmed and defeated Green Leader and the soldiers of Green Company. Amidst the clone casualties, Ventress emerged from a boarding craft. On her way to the reactor room, she decapitated a surviving clone and took his comlink. Infiltrating via the ceiling vents, she descended into the reactor room, bypassing 327-T and a patrol led by a captain and another trooper, and successfully planted explosives.
Unduli and Gree moved to reinforce the clones in the hallways after Unduli tasked Tano, Argyus, and a squad of Senate Commandos with guarding Gunray. However, Ventress reached the detention level and attacked the guards, killing two Senate Commandos. Aware that Argyus needed to maintain his cover, she used the Force to shove the Captain into a wall before Tano engaged her. Following a brief exchange of insults, Ventress and Tano began to duel. Ventress outmaneuvered the young Padawan, deactivated the laser gate of Gunray's cell, and kicked Tano into it. Gunray quickly escaped the cell and reactivated the lasers, trapping Tano. However, before Ventress and Gunray could escape, Unduli and a group of clones arrived. Unduli freed Tano, and the two Jedi fought Ventress until she detonated the explosives in the reactor room, fleeing during the resulting chaos.
Despite regaining control of Gunray, Argyus reported extensive damage to the ship. While Gunray was returned to his cell, Unduli decided to pursue Ventress alone. Tano offered assistance, but Unduli instructed her to continue guarding Gunray. Unduli tracked Ventress to the reactor room but was injured in a surprise attack. Ventress slashed open a pipe, damaging Unduli's left eye. Nevertheless, Unduli held her own against Ventress, even taunting her and criticizing her technique.
Meanwhile, a worried Tano expressed her desire to help Unduli against Ventress. Argyus cleverly encouraged her to disobey her orders and offer aid. Tano arrived just as Ventress kicked Unduli and trapped her under debris, preventing a fatal blow. She freed the Jedi Master, and together they confronted Ventress. Ventress chose to flee, using her stolen comlink to signal Argyus to free Gunray. Argyus shot two remaining Senate Commandos and then engaged Gree in blaster combat. When Gree shot the blaster out of his hand, Argyus freed Gunray and used him as a human shield. When Gree informed Unduli of the betrayal, Ventress re-engaged the Jedi to prevent them from assisting Gree.
When Gree demanded that the unarmed Argyus surrender, Argyus shoved Gunray into Gree, capitalizing on the Commander's surprise to kick off his helmet and disarm him. Gree punched Argyus in the face, but before he could aim at him, Gunray grabbed a blaster and knocked Gree unconscious from behind. When Argyus signaled Ventress that Gunray was free, she escaped back through the vent, throwing a thermal detonator at the Jedi to hinder their pursuit. Argyus and Gunray hijacked a Consular-class space cruiser and picked up Ventress, who had escaped the Tranquility in an escape pod. As Argyus congratulated them on their success, Ventress decided to execute him.
After Jedi Master Mace Windu requested that she join the impending invasion of Geonosis in 21 BBY, Unduli informed her Padawan Barriss Offee that she would also accompany her. She also mentioned to Offee that Tano would be present on Geonosis as well, alongside her Master Anakin Skywalker. When Offee inquired if she had met Tano, Unduli replied that she had, and while Tano had inherited several of her Master's characteristics, she had assisted her in fighting Ventress during the rescue, making Unduli indebted to her. In response, Offee felt guilty for not being there to protect her own Master but expressed her gratitude that Tano had been there for Unduli.