Alone on a distant outpost, clone officers Rex and Cody must inspire their rookie unit to believe in themselves to stave off a droid commando invasion.

Anakin and Obi-Wan have been duped and are being held for ransom along with Count Dooku by the pirate chief Hondo Ohnaka and his second-in-command, Turk Falso. While Anakin, Obi-Wan and Dooku unsuccessfully attempt to escape, the Republic sends the ransom via a special envoy, including Representative Jar Jar Binks. When Falso tries to steal the ransom from his boss by shooting down the shuttle, the only survivors are a squad of clones and Jar Jar, who as the most senior officer alive, has to take charge of the mission. It becomes a race against time as Jar Jar rushes to deliver the ransom to take custody of Dooku and save the Jedi.

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...

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.