Anakin Skywalker and Obi-Wan Kenobi land on General Grievous (Invisible Hand) in a attempt to rescue the chancellor from the Sith Lords clutches. They reach the top of the ship where the chancellor is being held captive. They encounter and are confronted by Sith Lord Count Dooku himself. an intense lightsaber duel ensues. The Jedi throw the Count off guard, by converting from basic attacks to more skilled tactics. During the battle, Obi-Wan is rendered unconscious when Dooku uses the Force to hold him in mid-air by the throat before hurling him against a railing. Anakin ends the fight by severing both of Dooku's hands, rendering incapable of defending himself, and then holds him at blade point with both his own lightsaber and Dooku's weapon. Palpatine encourages Anakin to kill Dooku. At first, Anakin refuses but Palpatine firmly insists: completely unaware of Palpatine's true intentions, Anakin brutally decapitates the helpless Dooku.
At the Galaxies Opera House in the Uscru District, Anakin joins Palpatine in watching the Mon Calamari Ballet performing Squid Lake. Palatine tells Anakin that Clone intelligent has located General Grievous. Palpatine makes a remark about the tragedy of Darth Plagueis The Wise. Palpatine describes Darth Plagueis as a Dark Lord of the Sith so powerful and wise that he could use the Force to influence the midi-chlorians to create life. Not only this, but having such power and knowledge of the dark side, Plageuis could use this ability to save people he cared about from death, a statement which gets Anakin's attention (which was Palpatine's desire) and Palpatine describes the dark side of the Force as a pathway to many abilities considered by some to be unnatural. When Anakin asks what happened to Darth Plagueis, Palpatine concludes that Plagueis became so powerful that all he feared was losing his power which he eventually did. Unfortunately for Plagueis, he taught his apprentice, who happened to be Darth Sidious, all he knew: after he had, his apprentice killed him in his sleep. (The Sith apprentice in the story, as implied by the film and explicitly stated in various Star Wars Legends sources, is Palpatine himself.) Palpatine notes the irony of how Plagueis could keep others from dying, but not himself. When Anakin asks if it is possible to learn the power to stop death, Palpatine simply replies, "Not from a Jedi," further alienating Anakin from the Jedi Order
With the duel continuing fiercely Anakin runs in just as Windup disarms Palpatine. With both warriors balancing on the edge of the large window shattered during the duel. As Mace holds Palpatine at blade point, the Sith Lord unleashes a torrent of Force lightning. However, Mace deflects it with his blade, casting much of the energy back into Palpatine's body. Palpatine face becomes distorted and arouses many disturbing qualities. As mace decides to end Palatine reign Anakin interferes know that he needs him to save Padme by severing winds arm. Palpatine, cackling with glee, blasts the shocked Mace out of the window, sending him plunging to his death hundreds of stories below. Anakin is horrified by his actions, yet he knows now there is no turning back. He pledges allegiance to Palpatine, in return for the Dark Lord's power to stop death, in the hope of saving his beloved wife. Palpatine takes Anakin as his Sith apprentice, bestowing upon him the Sith name Darth Vader. Palpatine then gives Vader his first assignment: to launch an assault on the Jedi Temple, ensuring the so-called Jedi Rebellion is crushed.
Vader leads the 501st Legion to the Temple. He then rampages through the Temple, cutting down every Jedi that crosses his path, including swordsmaster Cin Drallig and even a group of Younglings hiding out in the Council Chamber.
with a group of shock troopers led by Commander Thire, Darth Sidious arrives on Mustafar to rescue Darth Vader. From the edge of death Darth Vader is rescued using a stasis-pod and Sith medicines held in Sidious's shuttle. On the isolated asteroid Polis Massa, Yoda meditates and hears the spirit voice of Qui-Gon Jinn. The voice tells him that there is a way to merge with the Force and retain consciousness after death. In order to learn this power, Yoda declares himself an apprentice to the spirit of Qui-Gon Jinn.
Obi-Wan arrives at Polis Massa with Padmé, who is given emergency medical treatment by the facility's droids. She is dying, having lost the will to live. The medical droids work to save her babies—she has twins, much to the surprise of Bail Organa, Obi-Wan, and Yoda. A boy and a girl are born. In her last few dying breaths, Padmé gives them the names "Luke" and "Leia." Vader gets reconstructed at The Grand Republic Medical Facility on Coruscant. Vader is given new legs, a new arm, mechanized lungs, and other "replacement parts". He is dressed in black armor, a face mask is sealed tightly, and his helmet is fitted. Darth Vader begins to breathe through his mask. Most, if not the entire surgery is carried out in true dark-side form, with Vader wide-awake and apparently unanesthesized, leaving him moaning, screaming, and writhing in excruciating agony. Padme's last words were saying "there is still good in him" referring to Anakin. With Vader being fully operational he comes to a standing position. Vader asks Sidious about Padme. The Emperor proclaim that Vader has killed Padme through his hate. Vader cries "Nooo!", and unleashes a powerful involuntary Force scream of rage, shame, and grief, shattering the droids and equipment.
On board the Sundered Heart, docked at Naboo, Obi-Wan, Yoda, and Bail Organa sit at a conference table. They agree to keep Padmé appearing pregnant, thus faking the children's deaths. For their own safety, Luke and Leia will be split up in hopes that the Sith would not sense their presence. Leia will be adopted by Bail Organa and Luke would be sent to his father's step family on Tatooine. Obi-Wan and Yoda will watch and wait until the time is ready for the Skywalker children to do their part. Yoda tells Obi-Wan to study the technique Qui-Gon learned to achieve immortality.
Bail Organa leaves R2-D2 and C-3PO in the care of Captain Raymus Antilles of the Sundered Heart. He orders a memory wipe of the talkative protocol droid.
On Naboo, Padmé's funeral takes place in a solemn ceremony in Theed. Her hands clasp the japor snippet given to her by Anakin following his departure from Tatooine some thirteen years previous. To protect her children, her body appears to still be pregnant.
Yoda heads to Dagobah to begin his self-imposed exile, which he partly owes as penance for his failure to defeat Sidious.
On the bridge of a gray-hulled Venator-class Star Destroyer, Vader, the Emperor, and Governor Wilhuff Tarkin oversee the construction of a moon-sized battle station.
On Alderaan, the infant Leia is brought by Bail Organa to his wife, Queen Breha.
On Tatooine, Obi-Wan brings Luke Skywalker to his new family: his uncle, Owen, and his aunt, Beru. Obi-Wan leaves on an eopie, heading to his exile in the Jundland Wastes. Owen and Beru, holding the infant Luke, look out to the horizon and watch the setting of Tatooine's twin suns.
Running down a hallway on Invisible Hand Obi-Wan, Anakin and Chancellor Palatine are caught by a ray shield trap. The three are bought to the ships bridge before General Grievous under custody, Anakin Droid RD-D2 successfully creates a distraction, allowing the Jedi to retrieve their lightsabers and break free. Accepting his defeat the General smashes a window with his fallen guard's electrostaff, and is swept outside. Using a tow cable, Grievous latches himself to the ship and heads for the escape pods. Launching all other escape capsules, Grievous speeds for the safety of a Trade Federation Lucrehulk-class battleship. Once again, the flagship begins to descend in a free-fall into Coruscant, but Anakin takes the controls and pilots the ship into a hard landing, aided by emergency firespeeders, on one of Coruscant's industrial landing platforms.
On Coruscant, Anakin is praised for his heroics. He meets secretly with Padmé Amidala, and they share a kiss in the shadows of the Senate office building, keeping their love secret. She reveals to him that she is pregnant with their child. Having escaped General Grievous arrives at the Utapau system to meet with the Separatist Council. The General is contacted by Darth Sidious, who gives him instructions to move the Separatist leaders to a volcanic planet, Mustafar. Darth Sidious informs Grievous that the war is almost over. Later, on Coruscant, Anakin awakens in a panic, covered in sweat. He reveals to Padmé that he has been dreaming about her dying in childbirth, and believing that he can't live without her, vows not to let this dream come true. Anakin is later accepted onto the Jedi council but does not receive the rank of Master Jedi.
Obi-Wan arrives on Utapau and begins his search for General Grievous, riding a varactyl named Boga. He finds Grievous on the Tenth Level. After Obi-Wan dispatches the droids around Grievous, the two engage in single combat. Grievous's arms split in half, allowing him to use four lightsabers at once. Obi-Wan quickly cuts off the lower halves of the General's hands, helping to even out the odds a little. During the battle, the Third Systems Army arrives under the command of CC-2224 (Cody). Obi-Wan manages to catch Grievous off guard and uses the Force to push the fiendish droid general into the ceiling. Grievous drops his remaining two lightsabers and attempts to flee on his wheel bike, while Obi-Wan pursues on Boga. During the chase, Obi-Wan drops his lightsaber, which Commander Cody happens to find during the massive battle against the droids. Obi - Wan catches up to Grievous and leaps onto his wheel bike. Using Grievous's electrostaff, he manages to destabilize the speeder, and it goes into a spin. Both Obi-Wan and Grievous are thrown off as the speeder topples over the edge of Grievous's secret landing platform. Grievous draws his blaster although it is knocked from his hands by Obi-Wan now wielding the electrostaff. He knocks Grievous down, and a brawl commences. Obi-Wan rips open the General's chest plate armor exposing his organs. General Grievous repeatedly hits Obi-Wan than throws him to the edge of the landing platform. Obi-Wan uses the Force to retrieve the General's blaster and fires at Grievous's exposed organs. He hits, and they burst into flames. With his eyes flaming, Grievous falls to the floor, dead.
Anakin returns to the Jedi Temple and approaches Windu who tells Anakin that they have just been informed that Obi-Wan has destroyed General Grievous and so they are going to go to the Senate to ensure that Chancellor Palpatine gives back his emergency powers. However, Anakin reveals that Palpatine is a Sith Lord and is not likely to give up his powers, a statement which shocks Mace and stops him dead in his tracks. Anakin confirms what he just said and says he believes Palpatine is the one they have been looking for. When Mace asks how Anakin knows this, he tells Mace that Palpatine knows the ways of the Force and has been trained to use the dark side and that he is absolutely sure. Mace says their worst fears have now been realized and that if the Jedi Order is to survive, they must move quickly. Anakin warns Windu that Palpatine is very powerful and they'll need his help to arrest Palpatine, but Windu urges him to stay out of it as he senses much fear in Anakin and it could cloud his judgment. Mace also adds that if what Anakin says is true then Anakin will have gained his trust but for now, he wants Anakin to wait in the Council Chambers until he returns. Masters Windu, Kit Fisto, Agen Kolar, and Saesee Tiin board a gunship and head to Palpatine's office. Sitting in the Council Chambers, remembering Palpatine's promise of stopping death and the dreams of Padmé dying in childbirth, Anakin ruminates over his decision: in his mind, he hears Palpatine's voice saying that if the Jedi kill him, any chance of saving Padmé will be lost. Finally, he leaves and rushes after the four Jedi.
Mace Windu and the three other Jedi Masters arrive at Chancellor Palpatine's office. Windu declares Palpatine is under arrest, and the Masters ignite their lightsabers. Palpatine pulls a lightsaber from his sleeve, and hurls himself at the Jedi with a screeching warcry. Agen Kolar is first to die, run through the chest. Almost immediately after, Palpatine turns and slices Saesee Tiin's torso, and a few seconds later, with more effort from Sidious, Kit Fisto is slain, killed by a slash across the gut. Only Mace Windu remains, alone against the Dark Lord.
Meanwhile, from his office, Palpatine broadcasts a command to the many clone trooper commanders spread throughout the galaxy: to execute Order 66, an action that is effectively set into motion.
Across the galaxy, clone troopers turn against their Jedi Generals. As this happens, Yoda feels everyone who is dying. On Utapau, Kenobi is flung off a cliff by a blast from an All Terrain Tactical Enforcer, but he and Boga survive the drop; on Mygeeto, Jedi Master Ki-Adi-Mundi is gunned down by CC-1138 and the Galactic Marines; on the lush, tropical planet of Felucia, Jedi Knight Aayla Secura is murdered by CC-5052 and his 327th Star Corps; on Cato Neimoidia, Plo Koon's Jedi starfighter is shot down by ARC-170 starfighters, sending it smashing into a clone staging area; and on Saleucami, Stass Allie's 74-Z speeder bike is destroyed by CC-8826 and his wingman, riding BARC speeders. On Kashyyyk, Yoda is overlooking the ongoing battle as Commander Gree receives the order. He and his lieutenant attempt to sneak up to Yoda, but the aged Master senses their intent and beheads both clones with a slash of his lightsaber. Tarfful and Chewbacca help Yoda escape the planet.
Senator Bail Organa arrives at the flaming Temple to witness the slaughter of a young Padawan named Zett Jukassa by a squad of troopers led by Commander Appo. Organa, horrified, flees the scene and departs Coruscant in the Sundered Heart, in an attempt to make contact with any surviving Jedi. Both Obi-Wan and Yoda survive Order 66, and are picked up by Senator Organa, having evaded pursuit. The Jedi decide to return to Coruscant to recalibrate the Jedi beacon calling for all Jedi to return to Coruscant, knowing that it's really a trap set by Palpatine. Instead, Kenobi hopes to warn any surviving Jedi to stay away from the Temple.
Following the attack on the Jedi Temple, Vader returns to Padmé at the Senate Apartment Complex, from where the smoke rising from the wrecked Temple can be seen. He tells her the Jedi have tried to take over the Republic, and there are traitors in the Senate. He asks for her loyalty to the Chancellor, then tells her that he will go to the Mustafar system, where the remaining Separatists have gathered, to end the war.
The star skiff lands on Mustafar, and Padmé is greeted by a smiling Vader. Padmé reveals her conversation with Obi-Wan; he tells her it is only lies, though he doesn't deny the accusations. Padmé begs him to run away with her to raise their child in peace. Vader, mad with power, counters by telling Padmé that he has brought peace to the Republic. He then states his intention to overthrow Palpatine so the two of them can rule the galaxy together. Padmé, realizing how much Anakin has changed, backs away in horror and tearfully begs him to stop.
As she pleads, Vader sees his former master Obi-Wan emerge from the star skiff. He then accuses Padmé of lying about her love for him and that she brought his former master to kill him. Confused and enraged, he Force chokes his wife: Obi-Wan orders him to let her go, which Vader subsequently does only after he has throttled Padmé into unconsciousness. Vader accuses Obi-Wan of turning her against him but Obi-Wan retorts that Vader has done that himself through his anger, greed, and lust for power. Vader states that he had brought peace, justice, and freedom to his "new empire" and offers Obi-Wan a reprieve so long as he stands aside; however, Obi-Wan maintains his loyalty to democracy. Snarling that those not with him are his enemies, Vader draws his lightsaber; with no other choice, Obi-Wan prepares to battle his former pupil. The two then break out into a ferocious duel of Student vs. Master.
In the Chancellor's holding office within the Senate Building, Yoda confronts Darth Sidious. They engage in an intense battle using their lightsabers and Force abilities. The duel brings them to the Grand Convocation Chamber, the heart of the Senate. Sidious hurls Senate pods at Yoda, and the effort to avoid them exhausts the Jedi Master. Sidious then blasts Yoda with Force Lightning, but with the last of his strength the Jedi master repels it enough to send both himself and Sidious over the pod's edge. Palpatine is able to hold on to a senate pod, while Yoda falls to the senate floor leaving only his cloak. With Bail Organa's help, Yoda flees the Senate Building, intending to go into exile.
The epic duel between Obi-Wan and Vader leads them through the Separatist stronghold on Mustafar. A missed slash from Vader's lightsaber damages a computer console, resulting in the deactivation of the bunker's shields. The duel continues as the entire facility is bombarded by lava, and both combatants ride down a lava river atop a collection arm severed from the main structure. Kenobi and Vader leap from the arm and continue their intense duel atop floating platforms. Obi-Wan makes one last appeal to his old friend, trying to convince him of Palpatine's evil, but when Anakin shouts that the Jedi are evil from his perspective, Obi-Wan roars back "WELL THEN, YOU ARE LOST!", accepting his student, friend, and brother is beyond redemption.
Though on the defensive throughout the fight, Obi-Wan eventually gains the high ground by leaping to the safety of a black sand bank, and in doing so, the upper-hand. Obi-Wan warns Vader that he now holds an unassailable position and begs him, out of a last vestige of friendship, not to try and continue the fight, but Vader, enraged and bloodthirsty, snarls, "You underestimate my power!" He recklessly leaps up to meet his old Master. In the blink of an eye, Obi-Wan performs a lightning-fast maneuver, severing Vader's left arm and both of his legs at the knees. Vader tumbles down the embankment and rolls to a stop at the edge of the river of lava.
As Obi-Wan watches in despair, Vader, now only being kept alive by his hate, tries in vain to pull his crippled, smoking body up the embankment with his remaining mechanical hand. Obi-Wan is overcome with disgust and sadness at the pitiful fate of "The Chosen One", and is reduced nearly to tears. He angrily shouts that Anakin has failed in his life and destiny, and has hurt all those who loved him, including Obi-Wan himself. Vader, now completely helpless and consumed by his dark-side emotions, can only scream in pain and powerless rage, cursing his former friend and Master. The lava below Vader then catches his leg, setting him on fire and horribly burning and disfiguring him. Obi-Wan, not willing to help his former pupil and best friend, or watch him die or kill him in cold blood, picks up Anakin's lightsaber and walks away. He returns to the star skiff and leaves the planet with the badly injured Padmé and her droids.
Anakin arrives on Mustafar and is greeted by Viceroy Gunray. Anakin traps the separatists and slays them all. The senate hold a meeting with Chancellor exaggerating over a plot of the jedi trying to overthrow the senate. Amidst thunderous applause, he informs the Senate that the surviving Jedi will be hunted down and defeated. He then states that "in order to insure the security and continued stability the Republic will be reorganized into the first Galactic Empire". Senators Amidala and Organa are simply shocked and look around. In the meantime, Obi-Wan and Yoda go to the Jedi Temple, slaying clone troopers and walking in disbelief through the carnage. Yoda notices that several of their fellow Jedi were cut down by a foe wielding a lightsaber. They recalibrate the Temple's signal to warn all Jedi to keep away from the Temple. At the Temple's control center, Obi-Wan looks into the security recordings. In disbelief, he watches Vader's slaughter of the Jedi. Yoda says they have no choice but to destroy the Sith; including Vader. Obi-Wan begs Yoda to let him take Palpatine; however, Yoda refuses, stating that Obi-Wan cannot win that fight. Yoda tells Obi-Wan that Anakin has been "consumed" by Vader, and he must put his "brother" out of his misery. Obi - Wan arrives at Padme's apartment hoping to gain knowledge of Anakins whereabouts. He meets Padmé and tells her that Anakin has turned to the dark side and killed the younglings in the Jedi Temple. Padme will still not give up the location of her husband. Obi-Wan leaves. Later, Padmé leaves Coruscant in her star skiff, departing for Mustafar to find her husband, and the truth. Unknown to her, Obi-Wan secretly stows away aboard the ship just before it takes off.