The Republic discovers a Separatist bio-weapon lab hidden on the planet of Naboo. Rather than wait for help, Padmé; explores the lab with Jar Jar. Anakin, Ahsoka, Rex, and Obi-Wan arrive and follow after her. They find that the Senator is being held captive by the sinister Dr. Nuvo Vindi. The mad scientist has been developing a lethal virus for the Separatists. Vindi threatens to set off a bomb and release the virus!

In an attempt to force the release of the crime lord Ziro the Hutt from prison, bounty hunters seize control of the Senate Building and hold members of the Senate hostage. Cad Bane, the leader of the operation, with the help of bounty hunter Aurra Sing, issues his demands to Chancellor Palpatine who has no choice but to meet his request. Unbeknownst to the hunters, Jedi Knight Anakin Skywalker is loose in the Senate Building.

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?

Jedi Master Eeth Koth is taken hostage and tortured by General Grievous. Anakin Skywalker, Obi-Wan Kenobi and Adi Gallia devise a daring rescue plan, but they soon realize the General has a plan of his own. The Jedi Knights and the Separatist general try to outmaneuver each other in a ship-to-ship and hand-to-hand battle high over the planet Saleucami.

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.

Desperate to turn the tide of a fierce battle on Malastare and win a strategic alliance with the Dugs, Chancellor Palpatine orders the Jedi to drop the Republic's newest super-weapon, an untested electro proton bomb. Unfortunately, the bomb's blast awakens an ancient and fearsome Zillo Beast, a monster of legendary size and ferocity. Now the Jedi must contain this deadly creature despite the interference of the bloodthirsty Dugs, who have their own agenda.

Boba Fett and his band of bounty hunters lead Anakin and Mace into a deadly trap on Vanqor. It's up to R2-D2 to journey back to Coruscant and warn the Jedi of their brethrens' peril. Battling beast and bounty hunter along the way, the trusty droid finally communicates his warning to Ahsoka and Plo Koon, who rush to Vanqor to save Mace and Anakin from a fiery death.

Padmé, on a diplomatic mission to Mandalore, guarantees the pacifist planet the Republic's full protection, but she and Duchess Satine soon find something sinister lurking beneath the planet's serene façade. Moogan smugglers have been sneaking in supplies, including bottled tea destined for the Mandalorian schools. To increase their profits, they have been diluting the tea with a hazardous chemical.

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.

Troubled by Asajj Ventress' growing prowess with the dark side of the Force, Darth Sidious commands Count Dooku to eliminate her. But Ventress survives Dooku's assassination attempt, and the jilted former apprentice vows to take revenge, enlisting the aid of her kinswomen -- the mystical Nightsisters -- in her sinister scheme. Mother Talzin, leader of the Nightsisters, veils Asajj and her fellow assassins in a cloak of invisibility, and they infiltrate Dooku's palace on Serenno. Though they fail to kill the Count, their use of captured Jedi lightsabers leads Dooku to mistakenly believe that the Jedi have tried to kill him. Interested in protection, he requests a new apprentice from Mother Talzin.

Anakin and Obi-Wan, sent to track down the mysterious figure behind the deaths of several Jedi, soon find themselves on the trail of the monstrous apprentice that Ventress has created: Savage Opress, who has been trained in the ways of the Sith by Dooku. When Opress returns to Count Dooku after an unsuccessful assignment, Ventress strikes. With Opress at her side, she attacks Dooku. Opress' loyalty is fleeting, however, and Dooku and Ventress discover that this new apprentice has a will of his own. When Savage returns to Mother Talzin, she gives him a new task: To seek the Outer Rim for his long-lost brother....