On a diplomatic mission to the planet Rodia, Padmé; discovers that her old friend and fellow Republic senator Onaconda Farr has allied his planet with the Separatists. In exchange for food and resources for his people, Onaconda captures Padmé and promises to deliver her to the Nute Gunray. Sensing Padmé is in trouble, Jar Jar Binks disguises himself as a Jedi, and with the help of C-3PO, courageously fights to rescue his friend and fellow senator.

Jedi Master Kit Fisto and his former Padawan, the Mon Calamari Jedi Nahdar Vebb, track escaped prisoner Nute Gunray to a remote world. Following Nute into a mysterious den filled with strange creatures, weapons, and war-time artifacts, the Jedi discover it is the trap-laden lair of General Grievous! Learning that Count Dooku has led the Jedi there in order to punish Grievous for his recent failures, the General is determined to prove his abilities and destroy the Jedi. Kit and Nahdar, along with a contingent of clones, must now fight their way past Grievous and his caretaker droid A-4D to avoid being caught in General's evil clutches forever.

With the space blockade around Ryloth destroyed, Obi-Wan Kenobi must lead a small clone force into a droid occupied town to sabotage their anti-aircraft guns. Obi-Wan's mission is complicated when he learns the town's inhabitants are being used as living shields. A pair of clones in his platoon forges an unlikely friendship with a refugee Twi'lek girl, Numa, who's been orphaned by the war. Through their relationship with her, the clones begin to understand the real cost of the war...

The battle for the Twi'lek homeworld of Ryloth rages as the Republic attempts to drive off the occupying droid army led by Separatist Leader, Wat Tambor. With his forces stretched thin, Mace Windu must convince Twi'lek freedom fighter, Cham Syndulla, to help him save the capital city from the droids' destruction. Initially, the Twi'lek hero is hesitant to aid Mace, but ultimately realizes the Jedi can be trusted and joins with him to liberate the city -- and ultimately the planet -- in the climactic battle.

Cad Bane has stolen a Jedi holocron which holds the secret locations of the galaxy's Force-sensitive children. Bane is tasked by Darth Sidious to kidnap several of the children to train as Sith spies. On one such kidnapping attempt, Bane is captured by Anakin and Ahsoka and brought before Obi-Wan and Mace Windu to have his mind probed. Unable to resist the combined Force powers of the Jedi, Bane agrees to lead Kenobi and Windu to his hidden base while Anakin and Ahsoka venture to Mustafar to save the stolen children from Darth Sidious' evil plot.

Zygerrian slavers are behind the sudden disappearance of an entire colony of people on the planet Kiros. As Anakin and Ahsoka rush to defuse a series of bombs planted by the slavers, Obi-Wan must fight with their imposing leader.

To locate the missing colonists, Anakin, Obi-Wan and Ahsoka go undercover to infiltrate the slavers on Zygerria. Anakin struggles with his emotions as a wily Zygerrian queen forces him to take questionable actions in order to carry out his mission.

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.