After Obi-Wan and Yoda view the security recordings of the Jedi Temple control center, and discover how Anakin has become Lord Sidious' treacherous apprentice Vader, Yoda declares: "Destroy the Sith we must." Although Obi-Wan initially refuses to kill Anakin and would rather kill the Emperor, Yoda insists that he has to fight his ex-apprentice young Skywalker, who has become "twisted by the Dark Side."
In her apartment, Obi-Wan informs Padmé of Anakin's evil transformation as the new apprentice of the Chancellor/Lord Sidious. Although anguished and disbelieving of the news, the very pregnant Padmé would not reveal Anakin's whereabouts, fearing that he would be killed. Obi-Wan hints that he knew they were married, and expresses his regrets. As she departs (with C-3PO) on her starship bound for Mustafar to find Anakin, Obi-Wan sneaks on board.
At Mustafar, Padmé relays Obi-Wan's conversation with her, but (without denying anything) Anakin/Vader claims Obi-Wan is trying to turn everyone against him. With his new powers, Vader thinks he can protect her, but refuses running away with her to leave everything behind, find peace and raise their unborn child. He thinks he has brought peace to the Republic, and could now overthrow the Chancellor so they could rule the galaxy together.
She is horrified when she sees his 'dark side' change, and confesses: "I don't know you anymore...You're going down a path I can't follow." When Obi-Wan walks down from the starship, Vader believes she has lied and betrayed him to Obi-Wan so that his former master could kill him. He begins Force-choking Padmé until she falls unconscious.
Obi-Wan accuses his former apprentice of bringing his problems upon himself by his lustful greed for power (he has been "The Chosen One" but has joined the Sith rather than destroying them), but Anakin/Vader refuses to stand aside and back down. Both draw their lightsabers for a climactic dueling struggle, representing the forces of the Empire's Dark Side against the democratic Republic - representing Peace, Justice, and Freedom.
A wild lightsaber strike of the computer console controls open the bunker shields, and they continue to fight perilously near the hot lava flows of Mustafar. During the fighting, Obi-Wan appeals one last time to his former apprentice, but when Anakin/Vader reveals he is not willing to view things differently, Obi-Wan yells: "Well, then you are lost!" On the "high ground" of a safe black sand bank, Obi-Wan gains the advantage, but Anakin/Vader thinks not: "You underestimate my power!"
However, as Anakin/Vader jumps to the sand bank, Obi-Wan - with a quick maneuver - severs his left arm and both of his legs at the knees. After being disarmed and crippled, the helpless, pained, and raging Vader curses at his former friend and Master. The river of lava near him catches his leg on fire, and he begins to burn. Not wanting to watch the death or cold-bloodedly kill him, Obi-Wan takes Anakin/Vader's lightsaber, and departs on the starship with the injured Padmé and C-3PO.
At the same time within the Chancellor's office in the Senate building, Yoda confronts the dark-hooded Darth Sidious. The dueling powers of the two Force Masters lead them into the Senate's Chamber, where intense fighting exhausts both of them and leads to a stalemate. With aid from Bail Organa, cloakless Yoda is able to escape and flee from the Senate, possibly to go into exile - to the isolated asteroid of Polis Massa. Darth Sidious flees to Mustafar, where Vader is found still alive. His charred, severely truncated body is resuscitated and brought back from death.
On a medical ship at Polis Massa, Padmé (although healthy) quickly deteriorates, due to a broken will and heart - an emergency operation saves her twin babies (a boy named Luke and a girl named Leia), but her life is lost. Her final words to Obi-Wan: "There's good in him. I know. I know there's still - "
A screaming and agonized Darth Vader is also being treated (without anesthesia) back in Coruscant. He is encased in a black armored life-support suit and helmet (or face mask), and fitted with new cybernetic (prosthetic) limbs and a mechanized respirator. After the reconstructed Vader is told by the lying Darth Sidious that he has angrily killed his own wife, he releases a tormented scream of "Nooo!" - and his involuntary Force powers shatter nearby droids and other equipment.
The film concludes with the following developments: In Naboo, it is decided that the two children should be kept safe from harm by splitting them up. Yoda promises training for Obi-Wan in the meantime, to teach him about "the path of immortality" - from one (the spirit of Qui-Gon Jinn) who has returned from the netherworld of the Force. Yoda goes into self-imposed exile on Dagobah. The two droids R2-D2 and C-3PO would be cared for by one of the Captains, and C-3PO's memory would be wiped. Padmé's solemn funeral ceremony is held in Theed. Her body is made to appear pregnant, to fake the baby's deaths and protect them.
On a large Star Destroyer vessel, Darth Vader and Darth Sidious observe the construction of the Death Star, a moon-sized battle station. Senator Organa and his wife Queen Breha adopt Leia on Alderaan. Obi-Wan delivers Luke for adoption to his father's step-family, Uncle Owen and Aunt Beru Lars on Tatooine. The Master Jedi would remain close by in exile in the Jundland Wastes.
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