After the Battle of Ryloth, Jedi Luminara Unduli and Aayla Secura discovered a hologram of a Munificent-class star frigate being destroyed by a gravitic polarization beam on Alzoc III. Further investigation by Anakin Skywalker revealed the culprit to be bounty hunter Cad Bane, who stole of the bombs from his rival, Kul Teska. Teska was planning to use the beam to destroy the Naboo sun and prove his worth to Dooku. Meanwhile, Senator Padmé Amidala, who was investigating a rumored Separatist base near Naboo, was kidnapped by Teska's droids. Discovering her disappearance, the Jedi Masters Obi-Wan Kenobi and Mace Windu, accompanied by Skywalker and his Padawan Ahsoka Tano, led an army of clones to infiltrate and destroy the laboratory.
Commander Cody and Captain Rex created a diversion while Jedi Generals Anakin Skywalker and Obi-Wan Kenobi sneaked into the droid facility and destroyed the shield generator, allowing the main body of troops, commanded by Mace Windu and Ahsoka Tano, to destroy the main building. Inside, Skywalker and Tano faced Kul Teska, while Rex, Cody, and Ponds brought the Twilight to the rendezvous point. While the three clone troopers were waiting by the Twilight, Dooku arrived. The clone troopers retaliated with blasterfire, but were force pushed to the inside of the Twilight. Dooku closed the freighter's doors and dropped an overhead piece of equipment on top of it with telekinesis. By the time Masters Kenobi and Windu arrived, the Count had already gotten away with it. After a short duel, Windu and Kenobi defeated Dooku. Before they could kill him, however, the platform they were standing on started to collapse. Mace Windu and Obi-Wan jumped aboard the Twilight that somehow either the clones or R2-D2 was able to keep from crashing. Dooku fell, only to be saved by Dark Acolyte Asajj Ventress piloting a Sheathipede-class transport shuttle, in which they escaped. Meanwhile, Skywalker and his Padawan had battled and defeated Teska (with some unexpected help from Cad Bane) and saved Senator Amidala before the duel, whom Anakin informed about a power regulator he and Ahsoka passed by on their way. Padmé later sabotaged the weapon via the power regulator. In the end, the Jedi and clone officers escaped with the Senator, leaving Teska and his experiments to die in the burning wreckage of the laboratory.