Plo Koon is sent to find the source of a distress signal sent to the Jedi Temple. Plo & his Bros search during a sand storm and find a ship that crashed ages ago. Plo discovers a lightsaber in the wreckage. Plo Spacetimes(™) the temple and tells them the ship belonged to long-lost Jedi Master Sifo-Dyas. The council reminds the viewers that Sifo-Dyas was the one who ordered the production of the clone army without the blessing of the council or the senate. 

Sifo-Dyas was sent to Falucia to negotiate a peace and he was killed there. No one knows what happened to his body since the Chancellor has ordered the files sealed. Yoda sends Obi-Wan and Anakin to Felucia to investigate, while he himself speaks with Chancellor Palpatine. Palpatine tells Yoda the prior Chancellor Valorum sealed the files. Valorum tells Yoda that Sifo-Dyas was to speak with the Pykes, a group that runs the spice trade, and he locked the files so that news didn’t get out; as speaking with the Pykes would be like negotiating with the Taliban in the aughts. Based on Palpatine’s comments, Yoda believed a second Jedi was with Sifo-Dyas, but Valorum assures Yoda that only his personal aide, Silman, accompanied Sifo-Dyas.

Palpatine, as Sidious, Spacetimes(™) Dooku to have him cover his tracks and stop the Jedi investigation on Felucia. Obi-Wan and Anakin speak with the Pykes, after some Jedi persuasion the Pykes admit they shot down Sifo-Dyas’ ship and gave his body to Lord Tyranus, but kept Silman alive and imprisoned.

The Pykes offer Silman (now a crazy loon after all this time in solitary) to the Jedi to settle the affair. Meanwhile, Dooku shows up on Felucia, fights his way through some guards, and force-chokes Silman while literally standing right behind Obi-Wan and Anakin. A lightsaber duel ensues, during which it is revealed that Dooku is Tyranus! Dooku escapes.

The boys inform the council of what they discovered. Yoda tells everyone they must keep it a secret so as not to discredit the creation of the clones and the war effort.

The Jedi have leared that Dooku is the person who ordered the clone army: Yoda is meditating on this knowledge when he hears the voice of Qui-Gon Jinn, who explains that he has become part of the living force. Yoda informs the council and they all meditate together, but no one else hears the voice from beyond.

In order to determine if the voice is truly from the Force, or a trick by the Sith, Yoda undergoes a meditative trance/induced coma in a sensory deprivation tank. Yoda sees a vision of a swamp planet and the voice of Qui-Gon tells him he must go to Dagobah to complete what Qui-Gon could not. Skywalker escorts Yoda to a hangar, where R2-D2 and Yoda depart for Dagobah in a fighter.

R2 stays with the fighter in a desperate attempt to avoid any issues with him being on Dagobah with Master Yoda and knowing both how to get there and exactly who Yoda is. Yoda speaks more with Qui-Gon, who explains that he is now outside of linear time, like the Prophets of Bajor or Dr. Manhattan. Yoda sees visions of the dark future to come. Qui-Gon explains that Yoda he has been chosen to learn how to become part of the Force after death, as Qui-gon was, so that he can be a voice of light in the times to come. Yoda departs Dagobah, letting the Force guide him towards the origin of life in the Galaxy.

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