Anakin Skywalker and Obi-Wan Kenobi are thrust into a fierce conflict aboard the Invisible Hand, the flagship of General Grievous, who has kidnapped the Supreme Chancellor, Palpatine, high above Coruscant. After an intense battle with droids in the main hangar, they ascend the elevators to reach the general's quarters, where Palpatine is confined. However, they soon find themselves facing Count Dooku, Grievous' master. In the ensuing duel, Obi-Wan is knocked unconscious, and in a moment of rage that defies Jedi principles, Anakin brutally kills Dooku by driving his lightsaber through him.
The two Jedi manage to rescue Palpatine but are soon recaptured and brought before Grievous on the ship's bridge. They manage a daring escape as the ship, severely damaged, capsizes in orbit. Fighting off Grievous' bodyguards, Anakin ultimately crashes the ship on Coruscant, saving everyone on board.
Meanwhile, Obi-Wan embarks on a mission to Utapau to locate Grievous. He confronts the villain just as the Separatist council relocates to Mustafar for safety. During an epic duel amidst the chaos of invading Republic Army clones battling droids, Obi-Wan triumphs by impaling Grievous, ending his threat.
On Coruscant, Anakin discovers Jedi Master Mace Windu, who is about to finish off Palpatine, now revealed as the Sith lord Darth Sidious. In a twist of fate, Anakin, believing Palpatine holds the key to his power, intervenes, confronting Windu and ultimately stabbing him before throwing him out the window. This dark moment solidifies Anakin's allegiance to the Sith, with Palpatine bestowing upon him the title "Darth Vader." He is commanded to eliminate all Jedi at the Temple, where he begins a massacre, including the killing of librarian Jocasta Nu, as he turns against his former allies.
As the sinister plan unfolds across the galaxy, clone troopers follow Palpatine's orders and betray their Jedi generals. Despite the onslaught, Obi-Wan manages to escape from Utapau, only to learn that Anakin has become Vader. Driven by desperation to confront his fallen apprentice, Obi-Wan discovers Anakin's Sith transformation through security recordings and heads to Mustafar.
The former friends engage in a harrowing lightsaber duel amid the lava flows that engulf the Mustafar facility. With intense emotions fueling their fight, Obi-Wan demands Anakin surrender. However, in a moment of recklessness, Vader leaps over Obi-Wan, who seizes the opportunity to sever Anakin's limbs, leaving him to burn in the lava. Picking up his fallen lightsaber, Obi-Wan departs, leaving Vader for dead.
Palpatine soon arrives to find the injured Anakin yet alive, and he has him surgically enhanced, encasing him in the iconic black suit. Together, they oversee the creation of the Death Star as the Republic crumbles and the Empire rises.
In an alternate ending exclusive to certain video game versions, players witness a different fate for Vader. During the climactic battle against Obi-Wan, players can choose to play as Vader and triumph over his former mentor, showcasing a darker path where Anakin fully embraces his power, kills Obi-Wan, and takes his place as the Emperor’s apprentice. However, the GBA and DS versions adhere to the canonical narrative of Anakin's defeat, culminating in his revival in a mechanical suit under Palpatine's command.
