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.

Anakin, Obi-wan, and Ki-Adi-Mundi lead an invasion to stop Poggle the Lesser and the Geonosians from rebuilding their droid army. Things go terribly awry when Geonosian forces shoot down the Republic ships, which crash off-course. Under mounting pressure to accomplish their mission, Anakin, Obi-Wan, and Ki-Adi-Mundi each have their own set of challenges to overcome -- hordes of enemy troops, deadly traps, unforgiving terrain, and a massive energy shield.

Anakin, Ahsoka, Luminara Unduli and her Padawan, Barriss Offee, lead a mission to destroy a droid factory on Geonosis. But Poggle the Lesser has other plans as he deploys his newest weapon, the indestructible super tanks. Desperate to accomplish their mission before the foundry comes online, the Jedi devise a daring plan in which Anakin and Luminara will act as decoys, diverting the super tanks, while Ahsoka and Barriss infiltrate the plant via a labyrinth of catacombs beneath the city. The plan is risky. The stakes are high. It's their only option, but are the Padawans up to the challenge?

After a battle to destroy a new droid factory on Geonosis, Jedi Master Luminara Unduli disappears while tracking Poggle the Lesser. Obi-Wan and Anakin lead a platoon of clone troopers in search of her. Following her trail, our heroes descend deep into the lair of Karina the Great. To their horror, they learn that the hive is alive and teeming with undead defenders. Apparently, Karina can reanimate and control her subjects. Will Obi-Wan and Anakin overcome Karina's undead horde and find Luminara before it's too late?

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.