Master Yoda is meditating in his quarters when he hears a voice. When he asks who is speaking to him, the voice identifies himself as long-dead Jedi Master Qui-Gon Jinn, and claims to be speaking from beyond. When Yoda expresses doubt, he finds himself and any movable object in the room levitated, to his shock.
During a meeting of the Jedi Council, where Ki-Adi-Mundi makes it clear he believes that Dooku is merely the Sith apprentice, not the master, Yoda is caught off-guard when he is asked his opinion on the topic, as he has been thinking about the voice of Qui-Gon. After the meeting, Mace Windu has a word with Obi-Wan Kenobi about the incident, noting that he is concerned for Yoda's health.
Anakin Skywalker is entering the Temple courtyard when he hears a voice momentarily. He spots Yoda standing at the top of the steps, and asks him if he heard anything. Yoda asks him about when he saw Qui-Gon on Mortis. Anakin, surprised, asks if Yoda means to tell him that he's been talking with Qui-Gon. Yoda doesn't really respond to that.
Yoda tells the rest of the Jedi Council about the voice. He asks them for their help, and the entire Council gathers together in the center of the room to meditate, and see if they can find Yoda's voice. They do this for an entire day and night, conveyed through a truly awe-inspiring Time Lapse sequence. They find nothing.
Yoda finds himself sent to the medical bay, watched over by Dr. Nema. After some conversation, she suggests a deprivation ritual that might help Yoda find the source of the voice he's looking for. Yoda is duly lowered into a water tank, and his oxygen supply is lowered to bring him, in Dr. Nema's words, "as close to death as possible." Yoda has a vision, all right, in which Qui-Gon tells him not to do the ritual, and to go to Dagobah. After Yoda is hurriedly brought out of the tank, he's sent back to the medical bay, and Temple Guards are posted.
Obi-Wan, Ki-Adi-Mundi, and Mace have a conversation about what is going on. Ki-Adi is stridently convinced that what Yoda claims is absolutely impossible. Mace has to leave, because he's been called away to a meeting with the Chancellor because Yoda is indisposed. The Jedi Masters agree to keep Yoda under supervision for the time being.
Anakin goes to the medical bay because Yoda wanted to see him. It turns out that what he wants from Anakin is assistance in escaping, because "disobeying the Council, your expertise is." Anakin takes Yoda on a walk to the hangar, as instructed, and tells R2-D2 to get Yoda to his starfighter. As Yoda takes off, Mace and Dr. Nema run into the hangar, and Mace demands that Anakin explain himself. His response?
Yoda arrives at the planet Dagobah, and is greeted by the Force spirit of Qui-Gon Jinn in the form of a swarm of glowing lights, who explains that he can't take human form because his training to survive after death was incomplete. He guides Yoda to a cave strong with the Dark Side. Inside, he tells Yoda, the answer to his question of who the Dark Lord of the Sith is will be answered. The cave gives Yoda visions of Jedi fighting clones and Jedi being slaughtered. Above it all rises the blood-red specter of a hooded figure, who gives his name as "Sidious" and gives Yoda the offer to join him. Yoda refuses, and the spectral Sith Lord ignites his lightsaber. Yoda finds himself tumbling out of the cave. He asks Qui-Gon about it, and is told what he felt in that cave is only a fraction of the Dark Side's current power, and that the war cannot be won the conventional way.
Yoda is told that the Force will guide him to the next stop on his journey, and he and R2 take off.
- Agent Scully: Ki-Adi-Mundi is quite insistent that it's impossible to retain individuality after death, and that Yoda cannot possibly have been speaking to Qui-Gon.
- Call-Back: Yoda asks Anakin about his encounter with Qui-Gon on Mortis in "Overlords". Also, Qui-Gon describes midi-chlorians again, as creations of the Living Force.
- Dagobah, the Cave of Evil, and the Force spirit of Qui-Gon Jinn all make appearances. Yoda is set on the path to learning how to survive after death.
- Yoda sees visions of the deaths of Kit Fisto, Agen Kolar, Saesee Tiin, Mace Windu and Shaak Ti. The first four are shown in Revenge of the Sith whereas Ti's death at Darth Vader's hands takes place in a deleted scene.
- Godzilla Threshold: The "deprivation ritual" is extremely dangerous, as it brings a Jedi "as close to death as possible", but Yoda decides that it is the only way to get the answers he seeks.
- Hearing Voices: The other Jedi, most notably Ki-Adi-Mundi, think Yoda is doing this.
- Humble Hero: Yoda has no difficulty asking for guidance from the rest of the Council and is ready to admit that, rather than hearing Qui-Gon, he might be experiencing a deceptive attack from the Sith.
- Impaled with Extreme Prejudice: In the vision granted by the cave, Yoda sees Shaak Ti killed like this. Later on, the canonical Galactic Atlas would confirm she really did die that way.
- Internal Reveal: Yoda finds out the Sith title of the mysterious Dark Lord.
- I See Dead People: Yoda has a conversation with Qui-Gon, who can only appear as a disembodied voice. He doesn't appear to any of the other Jedi except Anakin, briefly, who doesn't realize what he heard.
- Mind over Matter: Qui-Gon can still do some telekinesis despite being dead, and he uses it on Yoda to prove that they're really talking.
- Mythology Gag: Yoda's personal spaceship is a tiny little thing that is strongly reminiscent of a TIE fighter.
- Not Me This Time: Mace assumes that Anakin in some way came up with Yoda's escape. No, Yoda came up with it and shanghaied Anakin into helping him.
- One-Word Title: "Voices".
- The Patient Has Left the Building: Yoda has been confined to the medical bay because the other Jedi are worried about him. He enlists Anakin to help him escape.
- Poltergeist: Qui-Gon's posthumous levitation of Yoda and the contents of his quarters has this feeling.
- Satanic Archetype: The specter of Darth Sidious looks rather demonic, what with being blood-red and looming over Yoda and all.
- Time Lapse: There is an amazing sequence when the Jedi Council meditates, showing that an entire day and night pass in the meantime, with the camera circling around the Jedi Temple and showing the sun rising and setting, while non-stop traffic whizzes by.
- The Voice: As a result of his training being incomplete at the time of his death, Qui-Gon can usually only manifest as a disembodied voice. He can only do the typical blue glowing apparition on places like Mortis.