Ahsoka and Jedi Master Luminara escort the captured notorious Separatist leader Nute Gunray to Coruscant so he can stand trial for his crimes. However, they are unaware that Count Dooku has sent his assassin, Asajj Ventress, to free their captive. With the help of Senate Commandos, the Jedi have to thwart Ventress's efforts to free their prisoner, despite the traitorous plans of Senate Guard Captain Argyus.

Cad Bane has been hired by Darth Sidious to steal a Jedi holocron. The holocrons -- data storage systems that can only be opened through the Force -- are protected within a vault inside the Jedi Temple. Recruiting a changeling posing as a Jedi in his plot, Bane infiltrates the building's security systems and leads Anakin, Obi-Wan and Ahsoka on a chase.

The Jedi remain stranded on Mortis, and the Son, aligned with the dark side of the Force, renews his efforts to convert Anakin as the Jedi prepare for a decisive confrontation. Anakin is stunned by images of his dark future. The Son promises him the power to avert this destiny. The Father recognizes that the Son has broken the rules of time. He wipes Anakin's memory of these future visions, and steals the Mortis Dagger to end the conflict. The Father impales himself, thus preventing the Son from stealing his power. The Son, stunned by this, is run through by Anakin. With all three Force-wielders destroyed, the imbalance in the Force disappears on Mortis. The three Jedi are transplanted back to the galaxy proper, apparently at the moment that they disappeared.

When the leader of the Gungans, Boss Lyonie, is injured it's discovered there is an uncanny resemblance between the Boss and Jar Jar Binks. Binks must sway his people from rising against the Naboo and stopping a Separatist invasion led by General Grievous.

Anakin tries to convince the Zygerrian Queen that she too is a slave and pawn in an evil Separatist plot. Meanwhile, Obi-Wan toils in the slave camps of Kadavo, a grim situation that grows increasingly bleak.