The story opens with Anakin and Obi-Wan returning from a space mission to find Coruscant under attack by a Separatist fleet under the command of General Grievous and Count Dooku, and that Chancellor Palpatine has been kidnapped. They fight their way onto the ship, fight across the ship, and then fight Count Dooku, who is holding Palpatine. Obi-Wan is knocked out, and then Palpatine (whom we the audience have finally learned really is Darth Sidious, but Anakin has not) urges Anakin on in his fight against Dooku. Anakin kills Dooku in the duel. There's some more running around, and a confrontation with Grievous (who then escapes) before Anakin flies the remnants of the ship into a controlled crash on the planet. Anakin, Obi-Wan and Palpatine all walk away (though Palpatine's plan was to have Obi-Wan die in front of Anakin).

Palpatine is calling for even more powers, and the Senate is prepared to give them to him. He wants, in particular, immediate and direct control over the Grand Army of the Republic and control of the Jedi. The Jedi, of course, don't want to let him have either, and are trying to find ways to stymie him. A group of Senators, led by Padme Amidala, is also trying to reign in Palpatine's powers, and presents him with a petition asking him to return his powers to the Senate. Palpatine names Anakin as his representative on the Jedi Council, which makes everyone more unhappy and increases tensions.

Grievous is discovered to be on an out-of-the-way planet on the Rim, and Obi-Wan is sent, alone, to bring him in. Anakin is annoyed that the "team" is being broken up. Yoda is also sent out on a mission, to the Wookiees' planet. The war would seem to be winding down, but Palpatine shows no signs of allowing that, and wants to turn the screws tighter -- he rejects Jedi calls for peace negotiations.

Anakin has been distracted since he's had prophetic dreams of Padme dying in childbirth, and his previous dreams have always come true. Palpatine strings Anakin along with stories of great Sith knowledge, and the potential to save her life, and eventually reveals himself as Darth Sidious. Anakin returns to the Jedi Temple and tells Mace Windu who Palpatine really is. Windu immediately grabs the three strongest Jedi there, and goes off to "arrest" Palpatine. Palpatine tapes the confrontation, making himself seem weak and helpless, then kills the four Jedi and starts his immediate purge of the Jedi, getting Anakin to do much of the work at the Jedi Temple, backed up by clone soldiers, who across the galaxy are having their secret "kill all Jedi" orders revealed. Palpatine stuns the Senate the next morning with news of what he calls a Jedi attempt on his life, and declares the beginning of the first Galactic Empire.

Obi-Wan and Yoda both survive, though no other Jedi are seen to live through the assault. They both make their way back to Coruscant, where Obi-Wan meets with a practically-in-labor Padme. Anakin has, at the same time, been sent off to yet another hole-in-the-wall planet to kill the remaining Separatist leadership. Obi-Wan rushes off to confront him, while Yoda confronts Palpatine simultaneously. Yoda is defeated by Palpatine but manages to escape, with the help of Senator Bail Organa. Padme had chased Anakin to his planet, and they are quickly joined by Obi-Wan. Anakin is jealous of Obi-Wan, who he thinks might have something going on, on the side, with Padme. Padme is left unconscious, and the two Jedi fight. Obi-Wan eventually wins, with Anakin left legless and armless near a lava flow. But Obi-Wan has to flee, because Palpatine is rapidly approaching in his ship. He runs away with Padme, who gives birth to twins and dies on board Bail Organa's ship. Organa will take the female twin, Leia, to raise as his own daughter. Obi-Wan takes the boy, Luke, to live with Anakin's relatives on Tatooine. Yoda insists that they not be trained as Jedi in any way whatsoever.

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