While negotiating Count Dooku's ransom, Anakin and Obi-Wan are taken prisoner. The Jedi and Sith form an unlikely alliance in a bid to escape, with Jar Jar Binks as their only hope.
Anakin is injured while rescuing Aayla Secura from Super Battle Droids equipped with rocket packs. Ahsoka crash-lands their shuttle on the neutral planet of Maridun, where the native Lurmen villagers refuse to takes sides in the war.
While the Jedi combat a new Separatist weapon, the pacifist Lurmen must decide whether they will surrender or fight with Anakin, Ahsoka and Aayla Secura.
While investigating the disappearance of a clone security force, Anakin and Obi-Wan get caught in the middle of a conflict between the territorial inhabitants of a desolate ice world and the greedy representatives of a nearby moon.
Anakin and Obi-Wan discover evidence of a traitor amongst their ranks while attempting to lead Republic forces to liberate Christophsis from a Separatist siege.
Evil scientist Dr. Nuvo Vindi is recreating the dreaded Blue Shadow Virus in his secret underground lab on Naboo. When he captures Senator Amidala and Jar Jar Binks, Anakin and Obi-Wan mount a rescue operation.
The fatal Blue Shadow Virus is released, infecting Ahsoka, Padmé and many clone troopers. Anakin and Obi-Wan must find the antidote on a mysterious planet from which no visitor has ever returned.
The Separatists have invaded the Twi'lek home planet of Ryloth. Anakin and Ahsoka lead a squadron of fighters against a Trade Federation battleship commanded by Neimoidian Captain Mar Tuuk.
To sabotage a powerful Separatist weapon, Obi-Wan and a small clone force enter an occupied town, and discover that its residents are being used as a living shield.
Mace Windu and his clone troopers aim to liberate the Ryloth capitol of Lessu but needs to acquire the help of a Twi'lek resistance group led by Cham Syndulla in order to do so.
To free crime lord Ziro the Hutt, bounty hunters seize control of the Senate Building and take hostages, unaware that Anakin Skywalker is still inside.
Luminara and Anakin act as decoys to divert new enemy super-tanks, while Padawans Barriss Offee and Ahsoka attempt to destroy a Separatist droid factory.
Luminara Unduli disappears during a sandstorm while following Poggle the Lesser. When Anakin and Obi-Wan track her to an ancient temple, they are attacked by undead Geonosian warriors.
Ahsoka, Barris and Tango Company board a supply ship to a station near Ord Cestus. But one of the troopers has been infected by a Geonosian brain worm and has taken along a nest full of worm eggs to submit the others.