General Grievous uses his latest weapon, the Malevolence, to destroy Plo Koon's fleet. Stuck in an escape pod with three clone troopers, Koon fends off more battle droids while Anakin and Ahsoka mount a rescue mission.
The Malevolence has been revealed to the Republic. Anakin and Shadow Squad, accompanied by Ahsoka and Master Koon, launch an attack in their new long-range Y-wing bombers.
Padmé Amidala and C-3PO are taken hostage by Grievous aboard the Malevolence. Anakin and Obi-Wan board the ship to rescue the senator and her protocol droid.
Alone on a distant outpost, Commander Cody and Captain Rex must inspire the rookie clones to believe in themselves to stave off a commando droid invasion.
Anakin, Ahsoka and replacement droid R3-S6 embark on a dual rescue/sabotage mission when they discover R2-D2 is being held at General Grievous' secret enemy listening post.
Padmé travels to Rodia to meet with old family friend Onaconda Farr about the lack of food rations. Unfortunately Farr has just made a deal with the Separatists. Padmé is imprisoned, leaving it up to Jar Jar Binks and C-3PO to rescue her.
Ahsoka and Master Luminara escort captured Nute Gunray to trial, unaware that Count Dooku has dispatched his deadly apprentice Asajj Ventress to free the prisoner and eliminate the Jedi.