Chancellor Palpatine was, in truth, Darth Sidious, Sith Lord. Yoda confronted Sidious in the heart of the Senate chambers. This erupted into an intense duel between these masters of the Force, a fight that Yoda ultimately lost and was forced to flee.

With the Galactic Empire triumphant, Yoda and Obi-Wan were the last of the Jedi. Yoda recommended hiding the children of Anakin Skywalker, for they held the hope for the future. Leia would live as the adoptive daughter of Senator Bail Organa of Alderaan. Luke would live on the Lars moisture farm on Tatooine, with Obi-Wan nearby. Yoda hid on Dagobah, where he studied the secrets of immortality by communing with Qui-Gon Jinn's Force spirit.

A generation after the Clone Wars, Yoda would once again train a Jedi. Luke Skywalker, Rebel hero and son of Anakin, came to the swamp world of Dagobah, seeking a Jedi Master. What he found instead was an impish creature. Luke misjudged Yoda, and quickly grew impatient with the bizarre misfit. This was Yoda's way of testing Luke, and already, the youth was off to a bad start.

Eager to learn the ways of the Force, Luke persevered. He longed to confront and defeat Darth Vader. Yoda warned Luke that the Force best serves a Jedi when he is calm and at peace, but Skywalker proved too impetuous. Despite Yoda's strict instructions to the contrary, Skywalker abandoned his training when he discovered that his friends were in danger. Yoda feared that Luke's recklessness would lead him to the dark side.

Luke emerged from his confrontation with Darth Vader battered but stronger. Returning to Dagobah to complete his training, an ailing Yoda told Luke the terrible truth that Vader was his father, Anakin Skywalker. Rather than destroy his father, Luke sought to bring him back into the light. At 900 years old, Yoda passed away, telling Luke that there was another Skywalker.

Luke's faith in his father proved to be well placed. Anakin returned from the dark side to destroy the Emperor. When Anakin died, he at last brought the Force back into balance. Using the knowledge imparted by Qui-Gon Jinn from beyond the grave, Yoda preserved his spirit in the Force, reuniting with Anakin and Obi-Wan as shimmering apparitions who witnessed the galaxy finally brought back to a state of peace.