A Jedi mission finds a lightsaber belonging to the long-dead Master Sifo-Dyas, prompting Yoda, Obi-Wan Kenobi, and Anakin Skywalker to begin an investigation into his decade-old disappearance. This sparks Darth Sidious to order Darth Tyranus to clean up any loose ends that may lead the Jedi to discover the truth of the Sith conspiracy.

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.

Letting the Force guide him, Yoda voyages into the heart of the galaxy to an ancient world that is one of the wellsprings of the Force and the source of midi-chlorians. Yoda undergoes difficult trials administered by the Five Priestesses, mysterious Force-wielders who hold the secret to immortality.

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.