The movie opens with a breathtaking space battle over the planet Coruscant. Chancellor Palpatine has been captured by the droid general, General Grievous. Anakin Skywalker and Obi-Wan Kenobi successfully break through the Separatist defenses and crash land in the hanger bay of the starship holding the Chancellor.
R2-D2 stays behind with the ships while Anakin and Obi-Wan go to locate the Chancellor. RD-D2 has to defend himself against some super battledroids as he aids Anakin and Obi-Wan in remotely operating doors and elevators. R2-D2 splashes oil on the battledroids and then ignites his booster rockets causing them to erupt into flames. Anakin and Obi-Wan eventually make it to the room where the Chancellor is being held and are confronted by Count Dooku. This time they agree to fight Dooku together and a three-way lightsaber battle ensues. Dooku uses his dark-side powers to throw Obi-Wan against a wall knocking him out. At the Chancellors urging, Anakin channels his anger into putting Dooku on the defensive and slices off Dookus hands. As Anakin holds 2 lightsabers to Dookus throat the Chancellor urges Anakin to behead Dooku, which Anakin does.
Although the Chancellor now wants to escape the ship leaving Obi-Wan behind, Anakin insists on carrying his mentor/friend. As the 3 make their escape they are captured in a ray shield and brought before General Grievous on the bridge of the ship. R2-D2 causes a distraction enabling Obi-Wan to use the force to retrieve his lightsaber freeing himself and Anakin. General Grievous flees the bridge and retreats in an escape pod. Kenobi and Anakin then dispatch some of Grievous henchmen and are left on a ship falling out of orbit and breaking in half. Anakin (the greatest star pilot in the galaxy) is able to successfully land the damaged ship on Coruscant.
Anakin is honored as a hero of the Clone Wars for saving the Chancellor from the clutches of the Separatist leader. At this time, Padme, who is lurking in the background, pulls Anakin aside to greet her secret husband after apparently many months of being away at battle. She informs him that she is pregnant, and Anakin says that he is very happy and they will deal with any issues and ramifications as they come.
We now have several scenes where the Jedi begin to show their distrust of Chancellor Palpatine because he has been reluctant to step down after his term is up, citing the need for continuing leadership for the Republic throughout the Clone Wars. Palpatine is able to use his political leverage to get Anakin appointed to the Jedi council, and the council reluctantly allows this but they do not grant Anakin the title of Master. The council asks Anakin to spy on the Chancellors doings although Anakin believes this to be treason against the Republic.
Anakin begins to have nightmares about Padme dying in childbirth, and he consults with master Yoda without going into specifics. Yoda advises him to not become too attached to anyone or anything that would cause him such distress if he were to lose them. Anakin vows to Padme that he will find a way to keep his nightmares from coming true, that he will stop Padme from dying. He could not do this for his mother, but he will do everything in his power to protect Padme.
Yoda, along with Clone troop support, is sent to the Wookie home planet of Kashyyyk to help defend against the robot armies of the Separatists. Yoda meets Chewbacca and other Wookie leaders.
Anakin attends a sort of space ballet performance with Palpatine in his private box seats. Palpatine seems to know that Anakin is troubled about Padme dying. He tells Anakin a story as a father would tell a son about a Sith Lord that was able to manipulate the force into causing life through midichlorians and was also able to stop people from dying. He taught these powers to an apprentice and the apprentice killed the Sith Lord in his sleep. Anakin is very intrigued by these powers and asked if it was possible to learn these powers. Palpatine replies, Not from a Jedi. Palpatine explains that the Sith also want peace in the galaxy, but they look to achieve it in a different manner than the Jedi. Palpatine asks Anakin if he has been told to spy by the council which Anakin admits to. Palpatine tells Anakin that he believes that the Jedi intend to kill him (Palpatine) to remove him from office. Finally, Palpatine reveals the location of General Grievous to Anakin to pass along to the Jedi. Killing Grievous may end the war.
Anakin informs the Jedi that General Grievous has been located on the sinkhole planet of Utapu. Although Anakin wants to take Grievous himself as he feels that he is more skilled than Obi-wan (having saved Obi-Wan from near death several times) the council determines that Obi-Wan will travel to Utapu along with clone troopers in order to defeat the droid general.
Later, Palpatine reveals to Anakin that he is the Sith Lord that killed his master. Anakin immediately draws his lightsaber towards Palpatine. Palpatine reminds Anakin that he has the knowledge to stop Padme from dying. Anakin decides to give this information to Jedi Master Mace Windu to decide the fate of the Chancellor.
In the meantime Obi-Wan has tracked Grievous to Utapu. Grievous has been meeting with all of the separatist leaders who are concerned about the death of Dooku.
Palpatine/Lord Sidious (we know for sure know that they are one in the same) assures the leaders that Dookus death was necessary in the big scheme and they will be safe on the lava planet of Mustafar. After the separatist leaders depart, Obi-Wan confronts Grievous and several henchmen and battledroids. Battles erupt everywhere on the planet between clone troopers and battledroids. Obi-Wan and Grievous have a lightsaber battle and Grievous is able to wield 4 lightsabers at a time. As Obi-Wan is able to successfully disarm Grievous he escapes on a motorized wheel. Obi-Wan pursues on a lizard-like creature jumping from level to level throughout the sinkhole environment. Eventually Obi-Wan catches Grievous and physically pries apart the protective metal covering Grievous internal organs. Obi-Wan then destroys Grievous with a blast from a laser gun exclaiming, How uncivilized!
As Anakin has told Master Windu about the Sith Lord running the Republic, he is told to wait in the Jedi chambers as he is too close to Palpatine to go on the arrest. Mace Windu is accompanied by 3 Jedi Masters to arrest the Chancellor. This is all falling into Palpatines plan as it seems that the Jedi are now attempting to overthrow the government. Palpatine confronts the Jedi with a red lightsaber and quickly dispatches 3 of them leaving only himself and Mace Windu to battle. Anakin, in fear that Palpatine may be killed and the knowledge of stopping death would be gone along with him, hurries to the Chancellors office to see this mighty battle in person. A window 20 stories up is shattered and although Mace Windu has the upper hand, Palpatine is shooting Sith lightening at Mace Windu and both are on the edge of exhaustion. Palpatine pleads with Anakin to help him, that the Jedi have come to kill him as he has thought. Mace Windu asks that Anakin help him to strike down this Sith Lord. Anakin wants Palpatine brought in on charges against the Republic, but Mace insists they take care of him now. Anakin cuts off Mace Windus hand which holds his lightsaber and Palpatines lightening knocks Mace out of the window to his death. Palpatines face has been disfigured by this confrontation (by the redirection of the lightening back on himself) and he now looks like the Emperor that we saw in Return of the Jedi. Anakin kneels before his new master and Palpatine anoints him Darth Vader. He warns Anakin/Vader that the Jedi will now begin to hunt them and they must rid the galaxy of all Jedi. Anakin/Vader is to go to the Jedi temple and destroy all Jedi- including the children. At the same time Palpatine announces via hologram to clone troops throughout the galaxy to enact Order 66. This order causes all clone troops to turn against the Jedi.
Apparently it was Palpatine who ordered the clone army and they have been programmed to turn against the Jedi at his command. We see a montage of shots on several planets where Clones turn against the Jedi killing them all. Obi-Wan and Yoda manage to escape. Yoda senses that something is not right and just as he is about to be shot from behind, he does a back flip and slices off the heads of the clone assassins. Yoda is then protected by Chewbacca and the Wookie general and leaves the planet on an escape pod.
Anakin is now marching on the Jedi temple with a legion of clone troopers. He finds a group of young Jedi in the temple who ask Anakin what they should do, there are too many of them (clone troops). Anakins only response is to ignite is lightsaber, implying that he destroys all of the children in the temple. Bail Organa drives a speeder to the temple as he sees smoke billow from it in the distance. He is turned away by clone troopers and sees them gun down a young Jedi. Bail manages to escape and pilots the Tantive IV (Princess Leias ship from the first Star Wars) to try to find any Jedi that are still alive. He picks up Obi-Wan and Yoda.
Anakin is told by Palpatine/Sidious to go to the lava planet of Mustafar and kill the remaining leaders of the Separatists.
Anakin briefly meets with Padme and tells her that he is going to Mustafar to destroy the remaining separatist leaders- the war will then be over and they can live together in peace.
Palpatine/Sidious goes before the Galactic Senate and tells of his assassination attempt by the Jedi which has left him disfigured. He declares all Jedi to be enemies of the Republic and announces that to keep peace and stability that he is creating the Galactic Empire and that he will be the Emperor. This is met with applause from the Senate. Padme remarks, So this is how democracy ends, with thunderous applause.
Yoda and Obi-Wan manage to find surveillance tapes of Anakin destroying the Jedi in the temple. Obi-Wan cannot believe what he is seeing. They know they must stop Palpatine and Anakin. Obi-Wan asks to face Palpatine because Anakin is too much of a brother to him. Yoda states that the Emperor is too strong for Obi-Wan to face, he must face the Emperor and Obi-Wan is to search his feelings and find Anakin.
Obi-Wan goes to Padmes apartment to tell her of the atrocities that Anakin has committed. She does not believe him, but he assures her that this is true. Obi-Wan reveals that he must kill Anakin. Although her pregnancy is concealed by her dress, Obi-Wan asks Padme if Anakin is the father. When she replies, yes, Obi-Wan states the he is truly sorry. Padme does not reveal where Anakin has gone, however.
Anakin/Vader arrives on the lava/volcano planet of Mustafar and kills all of the remaining separatist leaders.
Padme sets out to go to Anakin before Obi-Wan can reach him; however, Obi-Wan sneaks aboard her craft, and she inadvertently brings him along.
As Padme lands on Mustafar she is greeted by a happy Anakin who proclaims that he has brought an end to the war. Padme tells Anakin that she knows he has killed many Jedi. Anakin claims that Obi-Wan is lying and trying to turn her against him. Obi-Wan appears at the top of the exit ramp and Anakin goes into a rage. He is angered that Padme brought Obi-Wan to him and before she can explain that she knew nothing of this he force-chokes her to the ground.
Anakin and Obi-Wan then begin to square off in a fast-paced lightsaber battle. Intercut with this is Yodas confrontation with Sidious. Sidious knocks Yoda back with a lightening attack and then they both ignite their lightsabers. The battle begins in Palpatines chambers and then moves to the large Senate Hall. Both Yoda and Sidious throw the large Senate pods at each other. Yoda is eventually knocked several hundred feet to the Senate floor and manages to escape via a utility tunnel.
He is rescued by Bail Organa and Yoda exclaims that he has failed and must go into hiding until the time is right.
Anakin and Obi-Wan continue their duel throughout many locations on Mustafar. At one point they are fighting on floating platforms on a river of lava and Obi-Wan manages to jump to the bank. Anakin is going to attempt a much larger jump and Obi-Wan warns him that it is too far. Anakin exclaims that Obi-Wan has always underestimated him. As Anakin flips towards the bank, Obi-Wan slices off both of his legs at the knee and his left arm. Rather than show any fear, Anakin is still in a rage. The lava ignites Anakin clothes and he is burned throughout what is left of his body. Obi-Wan then goes to help Padme and he rendezvous with Bail and Yoda on the Tantive IV. They take Padme to a medical facility.
Palpatine, sensing that Anakin was in trouble, has come to Mustafar and finds him on the lava river bank barely alive. Anakin is transported back to Coruscant where he will be given the black armor of Darth Vader to sustain his life. The building of Vader is intercut with scenes of Padme delivering the twins Luke and Leia. Padme dies shortly after she names the children and her last words to Obi-Wan state that she believes there is still good in Anakin. The famous black helmet is lowered onto Anakin and we hear Vaders breathing apparatus kick in for the first time. Vaders first words to Palpatine are concern for Padme. Palpatine informs Vader that he killed her in his rage. Vader loses control and destroys everything in the room.
Yoda and Obi-Wan make plans to disappear until the time is right. Bails offers to take the girl, Leia, to his home planet of Alderaan. He and his wife have always wanted to adopt a girl. Luke is to be taken to his family on Tatooine. Yoda tells Obi-Wan that Qui-Gon has learned to become one with the force in spirit form and will train Obi-Wan to do the same.
Bail Organa orders C-3PO's memory to be erased (to keep the hiding of the twins a secret).
Vader, the Emperor, and a young General Tarkin look out from the bridge of a Star Destroyer at the Death Stars initial construction.
Leia is brought to Alderaan, and Obi-Wan delivers baby Luke to his Uncle Owen and Aunt Beru on Tatooine. They look out at the twin suns setting ..
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