Darkness on Dagobah! All attention is focused on Yoda, who claims to hear the voice of a long dead Jedi. Convinced that he is guided by Qui-Gon Jinn, he finds five Priestesses who will teach him how to manifest consciousness after death. After many trials, Yoda travels to Moraband, ancient home planet of the Sith. For now he must face the true evil that may be his undoing and one that seeks to control the galaxy....

Yoda's tiny starfighter emerges from hyperspace over the red world of Moraband, an ancient Sith world abandoned after many wars, ages ago. He pilots the craft into the Valley of the Dark Lords, a corridor of crumbling temples and tombs. Yoda has R2-D2 wait with the ship, and instructs the droid to contact the Jedi Temple if he does not return in three nightfalls.

Yoda arrives at the opening of the largest Sith temple as the sun begins to fall. A giant serpent, speaking in a sibilant voice, strikes but Yoda defends himself with the Force. From the shadows emerge the specter of undead Sith warriors that encircle Yoda, warning him that nothingness awaits after death. The spectral images slam into Yoda, leaving repercussions in the Force, but soon all is still. Elsewhere, in his command ship, Count Dooku awakens from meditation. He senses something. A tactical droid informs him that Darth Sidious has ordered him to return to Coruscant right away.

Yoda enters the largest of the Sith temples, illuminating his path with his lightsaber. At the end of a dark corridor is a cavernous chamber, at the center of which is the tomb of Darth Bane. A giant, smoldering specter of Bane, founder of the Sith rule of two, emerges from the sarcophagus and challenges Yoda. Bane wonders if Yoda has come to be his apprentice. Yoda resists reacting to the fiery image, declaring it to be nothing but an illusion.

Deprived of the power of fear and intimidation, Bane disappates. The call of the Priestesses echoes in the crypt, and Yoda follows the sound deeper into the temple.

In a burned out, industrial sector of Coruscant, Count Dooku's solar sailer sets down in a secret hangar. He is greeted by his Master, Darth Sidious, who senses a great opportunity to strike a deadly blow against the Jedi Order.

In the dark tomb on Moraband, Yoda enters a large chamber where the ancient Sith would sacrifice Jedi. The five Priestesses emerge before him and warn Yoda that the next trial is not of their doing -- it is instead created from the absolute darkness of this place, and it is not under their control.

On Coruscant, in a ceremonial chamber lined with statues, Sidious leads Dooku to a sacrificial altar basin. Sidious knows that Yoda is on Moraband. The Dark Lord explains that the strong Force-bond between Yoda and Dooku can be exploited to reach out through a ripple in the Force.

Producing a knife, Sidious cuts Dooku's hand, allowing a single drop of blood to fall into the water-filled basin. He and Dooku together zap the water with their Force lightning, while Sidious recites an ancient Sith incantation in the Balc tongue. Sidious dips his face toward the basin. He now wields the power of dark illusion, and will lead Yoda into a trap.

In the Moraband execution chamber, Yoda sees the withered form of Sifo-Dyas chained by lightning shackles to stone pillars. He begs to be released, offering in exchange the identity of the Sith Lord. Sifo-Dyas' mad eyes shine red and yellow. Yoda refuses the offer. Sifo-Dyas suddenly transforms into a cackling Sidious, and Yoda is surrounded by chains of energy.

The Jedi Master suddenly awakens in the hold of a gunship, flanked by clone troopers of the 501st and Anakin Skywalker. Yoda is disoriented; he is the midst of a mission. Anakin explains that a rogue shuttle slipped past the Coruscant security grid, and has been tracked to the industrial sector.

They believe Count Dooku is aboard, en route to meet with Darth Sidious. Yoda orders the mission to proceed. They are on the verge of discovering the identity of the Sith Lord. The Sith must not be allowed to escape. They must be executed.

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.