Valorum told Yoda that he sent Sifo-Dyas to negotiate with the to stop a booming drug trade underneath Coruscant. Valorum also revealed that he kept this secret, fearing his opponents in the bureaucracy. The talks were postponed after the Council sent Sifo-Dyas to intervene on Felucia. Valorum was unable to identify the second Jedi, but did say that his assistant, , was with Sifo-Dyas when he was shot down.
Sometime later, The Jedi received a distress single from a near . Sending Plo Koon to investigate, they found the remains of a shuttle and the lightsaber of Jedi Master , who was killed sometime around the while dealing with a conflict on . Upon reviewing the temple archives, and the Jedi found that the information had been sealed by order of the . While sending and his master, to Felucia, Yoda went to speak with , not knowing he was the Sith Lord that orchestrated the murder and the creation of the Clone Army. Palpatine told Yoda to visit as the events happened before the that got him to become Chancellor. Palpatine then contacted Count Dooku, telling him to destroy the last piece of the puzzle before the Jedi would be able to unravel the mystery.
In the final arc of the final season, Yoda hears Qui-Gon Jinn speaking to him from beyond the grave. Yoda flees the Jedi Temple with R2-D2 to travel to Dagobah, the planet he would make his home when he enters exile after events of , to find answers. Shown cryptic visions of the fall of the Jedi, Yoda learns he has been "chosen" to learn how to manifest his consciousness after death as a Force ghost. But Yoda is required to be tested by a group of spirit priestesses in order to overcome trials and temptations on his pilgrimage. During the final stages of his journey on Moraband, Yoda manages to pass the priestess' test of facing an illusion of . But Yoda's final test was to resist an attempt by Darth Sidious and Dooku to lure him to the dark side with a false vision of Sifo Dyas. After a lengthy metaphysical battle with Sidious, sacrificing himself to save Anakin's life, Yoda awakens from the vision and passed the test. He is told that Qui-Gon will teach him the means to manifest his consciousness after death while hearing what will be his last words, as well as the breathing of Darth Vader and the cries of his children. Yoda is informed his training will resume in time, and the elderly Jedi master is left with reassurance that regardless of what the future holds, there will still be a new hope.