The Republic gunship lands in the deserted tower used by the Sith Lords, and clone troopers and Anakin file out. Rex leads the charge, spotting the two Sith Lords huddled over the altar basin. Dooku ignites his lightsaber and electrifies the approaching clones with Sith lightning.

Anakin engages Dooku in a duel, while Yoda confronts the hooded form of Sidious. Anakin wounds Dooku, forcing him to his knees. Skywalker recovers Dooku's dropped lightsaber, and uses both his blue blade and Dooku's red blade to sever the Sith's head from his shoulders.

Sidious flees to a catwalk extending from the tower, and Yoda gives chase. The Dark Lord lights his blade, the two Masters engage in a whirling duel. Anakin rushes out to help Yoda, but runs headlong into a Force grip wielded by Sidious. Sidious blasts Anakin with Force lightning, sending the young Jedi crashing to the catwalk in a heap. He then blasts Yoda, who blocks the lightning with the Force. The discharge of energy rattles the catwalk.

Sidious uses his lightsaber to cut the support beams of the catwalk. The structure starts to collapse. As it cants forward, Anakin's unconscious body slides towards a deadly fall. Yoda halts his pursuit of the Dark Lord to catch Anakin with the Force. Sidious cackles at Yoda's predicament. Sidous tells Yoda to let Anakin fall, and thus thwart all of the Dark Lord's plans. Yoda refuses. Instead, Yoda drops his defenses to more fully concentrate on Anakin, thus sacrificing himself.

Yoda's body is blasted by Sith lightning, but he levitates Anakin to safety. Yoda hurls his lightsaber at the remaining struts of the catwalk, collapsing it, sending he and Sidious tumbling to their certain doom. Yoda grapples with Sidious as they fall, the Dark Lord cackling all the while. When Yoda grasps Sidious' cloak, he finds that it is empty. Sidious has vanished, and Yoda falls to the ground far below.

Sidious emerges from the glow of the sacrificial altar. The illusion has ended. Sidious has failed to break Yoda's spirit. The Sith Lords will need more time to defeat Yoda and the Jedi.

Yoda awakens in the execution chamber. The serene Priestess welcomes him. He has passed this challenge. The Priestess explains that Qui-Gon Jinn will commune with Yoda, and continue to guide his training. Through this study Yoda will achieve enlightenment, spirit, and balance. As the Priestess disappears in a glow of light, Yoda sees the future, including the moment of his death and his own last words.

Yoda emerges from the temple and returns to his starfighter, where R2-D2 awaits him. The ship leaves Moraband, and soon, Yoda stands beneath the great tree at the Jedi Temple. Mace Windu and Obi-Wan approach Yoda, so he can report to the Jedi Council. But Yoda cannot say much of his journey. He senses the war's end approaching, and knows there is no victory to be had in the Clone Wars. But another path to victory lies ahead for the Jedi, a path that is unknown to the Sith.