Jedi mystery! A lightsaber was found on the moon of Oba Diah belonging to Sifo-Dyas, the Jedi responsible for the creation of the clone army. The Jedi have learned that before the start of the war, Count Dooku murdered Sifo-Dyas and skillfully manipulated the Republic into the galactic conflict, intending for the Jedi to fight with the clones at their side. Now as the Jedi Council meets to discuss the purpose of this deception, Master Yoda meditates deep into the Force in search of answers....

Yoda sits in deep contemplation in the silent serenity of his quarters within the Jedi Temple. His concentration is broken by the sound of a familiar, yet impossible voice: that of long dead Jedi Master, Qui-Gon Jinn. Qui-Gon says he is part of the living Force, and proves his influence beyond the grave by levitating Yoda and causing some nearby candles to stir.

Later, during a Jedi Council meeting in which the Jedi Masters discuss the recent revelations about the Sith with great concern, Yoda is distracted. After the Council session, Mace Windu draws Obi-Wan to discuss his worries in private. Obi-Wan and Mace both sense great turmoil within Yoda, and wonder if he has reached his limits.

Yoda wanders to the training ground in the courtyard of the Temple, beneath the great tree. Anakin finds him there preoccupied with his thoughts. Yoda asks Anakin to describe his encounter with Qui-Gon Jinn on Mortis. Anakin believes that it was a trick, an apparition formed from memories, because Jedi knowledge states that an individual cannot retain his or her identity after becoming part of the Force. Yoda questions this ancient tenet.

After further meditation, Yoda addresses the Jedi Council. The old Master is shaken in his belief and his confidence. He asks the Council to meditate with him, to see if perhaps they too might hear the voice. The rest of the Council joins Yoda in meditation for an entire day. But as dawn rises anew, they all emerge from deep contemplation, having heard nothing. Ki-Adi-Mundi suggests a dark possibility: that Yoda might be subject to manipulations from the Sith. Yoda considers this, adding to his worries.

Yoda lies in a bed in the Jedi Temple medical ward, closely examined by sensors. Jedi Doctor Rig Nema finds nothing wrong with him. He is in great health for his age and species. Ki-Adi-Mundi posits the disturbing possibility that Yoda's past connection to Count Dooku has left him vulnerable to a Sith attack. In response, Nema suggests a deprivation ritual, a dangerous option that will allow Yoda to clear his mind and find the source of this haunting voice.

Anakin interrupts the discussion with word that the Supreme Chancellor would like to speak with Yoda in an emergency meeting. Mace goes instead, and leaves the decision regarding Yoda's treatment up to Yoda. The ancient Jedi Master agrees to Rig Nema's recommendation.

Yoda is suspended in a tank of dark liquid, where he will be induced into a deep state of meditation. The Jedi Master wears a small oxygen mask. Rig Nema begins deliberately lowering the flow of oxygen that will prompt the change of meditative state, bringing Yoda as close to death as possible. Obi-Wan and Anakin watch on with great concern.

In Yoda's mind, Qui-Gon's voice scolds him for taking the wrong path. A vision of a swamp world appears, and Qui-Gon implores Yoda to voyage to Dagobah, to complete the task that Qui-Gon could not. The disembodied voice warns Yoda to come alone, and to tell no one.

Yoda awakens to find himself pulled from the tank. The dazed Jedi Master was rescued by Obi-Wan and Anakin, who feared for his life. While Yoda recuperates, the Jedi reconvene in a private room -- Ki-Adi-Mundi, Obi-Wan, Dr. Nema, and Anakin confer with Mace Windu via hologram. Ki-Adi-Mundi is skeptical of Yoda's impossible claim of having spoken to the dead. He still worries that the Jedi Master is being manipulated by the Sith. As a precaution, Mace orders that Temple Guards be placed in the medical bay.

As Yoda recovers in bed, he calls for Anakin Skywalker to come to his side. With a grin, Yoda tells Anakin he needs the help of a spontaneous rule-bending Jedi if he is to escape. Yoda leaves his bed, and says to the guards that he is simply getting some fresh air. Anakin covers for the Jedi Master, assuring the guards he'll be under his supervision.

Anakin leads Yoda to the Jedi Temple hangar. He tasks R2-D2 to take Yoda to his ship and get him out of the Temple as fast as possible. The little droid jets over to a modified Jedi starfighter, and preps it for takeoff. Yoda boards the tiny craft and blasts away from the Temple. Mace Windu and Rig Nema come running in, furious at Skywalker. Anakin shrugs, explaining this was all Yoda's idea.

Yoda's fighter emerges from hyperspace over a cloud-shrouded jungle world. It pierces the dense canopy of trees and mist to land in a bog. Yoda tells Artoo to stay with the ship. The tiny Jedi Master walks into the swamps, finding a clearing to sit and meditate. The voice of Qui-Gon reaches out and greets Yoda.

He advises Yoda to follow a cloud of fireflies that will serve as a guide. As they travel, Qui-Gon explains that Dagobah is one of the purest places in the galaxy, and it allows for strong manifestations of the living Force. Qui-Gon himself is such a manifestation, but he had not completed his training to the extent that he could appear as more than a disembodied voice to Yoda.

Yoda asks if Qui-Gon can see the future, and if he might know who the mysterious Sith Lord is. Qui-Gon can only point Yoda to a cave entrance, where answers await. Yoda enters the cave, and is immediately surrounded by a vision powered by the dark side. Yoda sees horrible images of Jedi Knights struck down by a hooded Sith Lord. A face concealed by shadow cackles victoriously, and identifies himself as Sidious. He invites Yoda to join him, as there is no other way.

Yoda rushes out of the cave, and collapses in despair. The voice of Qui-Gon coaxes him to stand. Qui-Gon tells Yoda that he has seen only a glimpse of the darkness to come. Yoda wonders what hope there may be for the future, and Qui-Gon reveals he has been tasked with guiding Yoda forward.

The Jedi Master has been chosen, as Qui-Gon was chosen before him. Yoda will learn how to preserve his life Force, so he can manifest his consciousness and communicate with the living after death. Qui-Gon will guide Yoda to one of the origin-points of life in the galaxy, where he will begin his trials. Yoda returns to his starfighter, where R2-D2 awaits. His ship rises, ready to embark on the next step of his journey.