A Separatist blockade surrounds Christophsis. Anakin's fleet is tasked with deploying relief supplies to the surface but they are massively out-gunned and out-maneuvered by the skillful Admiral Trench. Obi-Wan arrives and unveils the Republic's new weapon: a stealth ship. The stealth ship is the last hope at besting the cunning Separatist fleet commander and aiding the battered people of Christophsis.

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.

As the Clone Wars sweep through the galaxy, the heroic Jedi Knights struggle to maintain order and restore peace. More and more systems are falling prey to the forces of the dark side as the Galactic Republic slips further and further under the sway of the Separatists and their never-ending droid army. Anakin Skywalker and his Padawan learner Ahsoka Tano find themselves on a mission with far-reaching consequences, one that brings them face-to-face with crime lord Jabba the Hutt. But Count Dooku and his sinister agents, including the nefarious Asajj Ventress, will stop at nothing to ensure that Anakin and Ahsoka fail at their quest. Meanwhile, on the front lines of the Clone Wars, Obi-Wan Kenobi and Master Yoda lead the massive clone army in a valiant effort to resist the forces of the dark side.