Anakin Skywalker and Obi-Wan Kenobi lead Republic forces in an attempt to defeat the droid armies and free the planet of Christophsis from the Separatist siege. When the Republic is ambushed and forced to retreat, it becomes clear that someone in their midst has set them up. The Jedi believe this infiltration is a Sith-backed operation and go behind enemy lines to investigate. Meanwhile, Captain Rex and Commander Cody set out to uncover the traitor amongst them.

The Jedi Council suspects that Senator Rush Clovis, an InterGalactic Banking Clan delegate and former colleague of Padmé Amidala, may be working for the Separatists. Against Anakin's wishes, the Council asks Padmé if she would accompany Rush to Cato Neimoidia to uncover any clues regarding the Senator's true allegiances. Padmé agrees, feeling that her past relationship with the Senator -- which for a time had been romantic until she ended it -- might give her an advantage in the investigation. Fending off Anakin's jealousy, as well as an attempt on her life by Neimoidian Lott Dod, Padmé successfully reveals Clovis to be conspiring with the Separatists to build a military droid factory on Geonosis.

Medical supplies are desperately needed for a crucial Republic battlefront. While the Jedi Knights transport Poggle the Lesser as a prisoner to Coruscant, the Padawans Barriss Offee and Ahsoka Tano are dispatched to escort the medical frigate to its destination. When Geonosian brain worms take control of the clone troopers aboard their supply ship, Ahsoka and Barriss must battle to stop the vessel from unleashing the deadly plague upon the galaxy.

During an assignment in the Coruscant underworld, a wily pickpocket steals Ahsoka's lightsaber. Ahsoka enlists the help of an ancient Jedi, Tera Sinube, to track down her weapon and reclaim her honor.

Alarming rumors about the peace-abiding Duchess Satine of Mandalore prompt Obi-Wan to investigate the secluded planet. Satine wants to keep Mandalore neutral in the Clone Wars, but the actions of a violent splinter group -- Death Watch -- threaten to push the planet towards war.

On Coruscant, word reaches Duchess Satine that Death Watch is mobilizing, sparking a pre-emptive Republic invasion. On the run from Republic authorities, Satine and Obi-Wan set off to discover the group's true motives.

When Senator Onaconda Farr dies under suspicious circumstances and the local Inspector appears incompetent, Padmé; sets out to find the person who poisoned her mentor. Following a trail of clues, Padmé and Bail Organa delve into a dangerous world of backstabbing, lies, and secrets controlled by the powerful Senators Mee Deechi and Halle Burtoni. Padmé's search forces her to risk her career and ideals but the true identity of the assassin is even more destructive than she could imagine.

Following a nefarious attempt to murder Anakin Skywalker and Mace Windu on Vanqor, Boba Fett and Aurra Sing go into hiding. Jedi Master Plo Koon and Ahsoka Tano set out to capture the bounty hunters. While combing through the lower depths of the Coruscant underworld, Plo and Ahsoka finally learn that Fett and his group are hiding out on Florrum. In a dramatic showdown, Fett is abandoned by Aurra Sing, leaving young Boba angry and bitter in Republic custody.

Ahsoka is assigned to teach a class at a leadership academy on Mandalore. Soon after she arrives, Duchess Satine's zealous nephew -- Korkie -- and his classmates uncover a nefarious plot. Prime Minister Almec is revealed to be an active part of the black market conspiracy on Mandalore, and he attempts to permanently silence Duchess Satine and the cadets before they expose his corruption. Ahsoka and the cadets defeat Almec before he can succeed.

Tasked to protect Senator Padmé Amidala during a political mission to Alderaan, Padawan Ahsoka Tano is plagued by recurring visions of recently-deceased bounty hunter, Aurra Sing. Unable to clear her mind, Ahsoka worries that the stress of conflict is finally getting to her until her visions indeed prove prophetic. Padmé narrowly avoids death when Aurra Sing attempts to assassinate her. Together, Padmé and Ahsoka trap the hunter, and Ahsoka discovers the true villain behind the plot to kill Padmé: the incarcerated gangster, Ziro the Hutt.