Using Duchess Satine as bait, Darth Maul lures Obi-Wan into a trap.

Clone trooper Tup succumbs to a mysterious mental illness that results in the shocking death of a Jedi Master. Unable to account for his murderous actions, Tup is sedated and sent back to Kamino for examination. Meanwhile, Admiral Trench of the Separatists informs Count Dooku of the betrayal, and is convinced that the killing stems from something deeper. Anakin Skywalker and ARC Trooper Fives accompany Tup, but their return trip is ambushed by Separatists.

Yoda is deeply unsettled when he hears something from beyond the grave: the voice of Qui-Gon Jinn. Knowing that it is impossible for a Jedi to retain his identity after death, the Jedi Council begins to worry that Yoda may be corrupted by the influence of the dark side. Determined to find answers, Yoda escapes the Jedi Temple to follow the disembodied voice.

After many grueling trials, Yoda next travels to the ancient Sith home world of Moraband, where he must face an ancient evil determined to rule the galaxy.