The Galactic Republic is crumbling in the midst of an epic war with the Confederacy of Independent Systems under the leadership of the Sith Lord, Count Dooku. The Confederate cyborg military leader General Grievous has swept into Coruscant and captured Chancellor Palpatine (as seen in the microseries Star Wars: Clone Wars and the James Luceno novel, Labyrinth of Evil).
As the droid army attempts to escape Coruscant, a huge space battle erupts with Jedi Knights Anakin Skywalker and Obi-Wan Kenobi leading a mission to rescue the Chancellor. The Jedi fight through the Separatist armada. In the process, Obi-Wan.s ship is damaged and the two Jedi crash into the hangar of the Trade Federation Cruiser, The Invisible Hand, the flagship of the Confederacy.
Anakin and Obi-Wan make their way through the Federation Cruiser, fighting through an army of droids. They reach the room where Chancellor Palpatine is being held captive by Count Dooku. A lightsaber battle ensues, with the two Jedi teaming up against Dooku. During the battle, Obi-Wan is rendered unconscious. Anakin continues the battle, gaining the upper hand and cutting off Dooku's hands. With Dooku on his knees, Anakin holds his (and Dooku's) lightsaber to Dooku's neck. With encouragement from Palpatine, Anakin beheads the helpless Count.
The Republic Venator-class Star Destroyer Guarlara launches a final broadside attack that mortally wounds the ship, and it begins to descend uncontrolled into Coruscant. Anakin carries the unconscious Obi-Wan on his back, and maneuvers through the ship with Palpatine. Obi-Wan later regains consciousness.
The three are captured by General Grievous. R2-D2 creates a distraction, allowing the Jedi to retrieve their lightsabers and break free. However, Grievous manages to escape, as well as release all the remaining escape pods. As the ship descends in a free-fall into Coruscant, Anakin takes the controls and pilots the ship into a hard landing.
On Coruscant, Anakin is praised for his heroics. He meets secretly with his wife, Padme Skywalker. They share kisses in the shadows, keeping their love secret. She reveals to him that she is pregnant.
Later, Anakin awakens in a panic, covered in sweat. He reveals to Padme that he has been dreaming about her dying in childbirth, and he vows not to let this dream come true.
Chancellor Palpatine requests Anakin's presence, and they meet in the Chancellor's Coruscant apartment. The Senate has granted the Chancellor further emergency war powers, giving him direct control of the Jedi Council. Palpatine confides to Anakin his fear, distrust, and contempt of the Jedi. He appoints Anakin to be his personal representative on the Jedi Council.
The Jedi Council accepts Anakin's appointment, but does not grant him the rank of Jedi Master. Anakin reacts angrily, insisting he is more powerful than anyone else on the council. The council goes on to discuss matters concerning the war. It is decided that Anakin will be assigned to protect the Chancellor, and Yoda will take a battalion of clones to reinforce the Wookiees on Kashyyyk. Anakin is angry and disappointed.
Obi-Wan later tells Anakin that the Jedi Council wants Anakin to report on all the Chancellor's dealings, essentially spying on him. Anakin is outraged, but accepts the mission.
At the Galaxies Opera House in Coruscant, Anakin joins Palpatine in watching the Mon Calamari Ballet performing .Squid Lake.. Palpatine continues to subtly manipulate Anakin, making him mistrust the Jedi. He also tells him of Darth Plagueis, a Sith Lord that used the Force to save people from death, but whose apprentice killed him in his sleep. Palpatine says the ability to save people from death is something that can be learned, but not from a Jedi.
The Jedi Council receives word from Palpatine that General Grievous is on the planet of Utapau. They decide to send Obi-Wan to Utapau. Anakin is upset that he was not chosen instead.
Obi-Wan arrives on Utapau and searches for General Grievous, riding a lizard-like creature called a varactyl. This particular one is named Boga. He finds Grievous and the two erupt in battle called the Battle of Utapau, with Grievous using four lightsabers at once. Grievous attempts to flee on a Wheel Scooter, and Obi-Wan pursues astride on Boga. During the chase, Obi-Wan drops his lightsaber.
On Coruscant, Anakin tells Palpatine that General Grievous has been found by Obi-Wan on Utapau. Anakin insists he should be on Utapau as well. Their conversation shifts to Palpatine's knowledge of the force, and it is revealed that he is the Sith Lord, Darth Sidious. Upon realizing this, Anakin ignites his lightsaber and threatens to kill Palpatine, but then decides to expose him to the Jedi Council.
Obi-Wan continues to chase General Grievous on Utapau. He catches up with the general, and the two engage in melee combat. Obi-Wan manages to grab and rip off General Grievous's loose chestplate, exposing the living organs in his chest. Obi-Wan retrieves the droid's blaster and shoots the general in the chest, causing him to explode from the inside out, killing him.
Anakin tells Mace Windu that Chancellor Palpatine is the Sith Lord, Darth Sidious, who they have been looking for. Anakin offers to help in Palpatine.s arrest, but Windu urges him to stay out of it.
Through the Force, Palpatine speaks to Anakin, telling him that if he dies, Padme will die in childbirth. Palpatine tells him that only with his help can she be saved. Anakin rushes to Palpatine.
Mace Windu, accompanied by Saesee Tiin, Kit Fisto, and Agen Kolar, arrive at Chancellor Palpatine's office to have the Chancellor arrested. Palpatine pulls a lightsaber out of his sleeve and lunges, quickly stabbing Agen through the chest. He pulls his lightsaber out of Kolar's chest and then slashes Saesee Tiin. He continues to duel Mace and Kit Fisto but eventually kills Kit by slashing him in the back and head too. Palpatine and Mace continue to fight down the hallway and into the main office area. Meanwhile, Anakin arrives at the scene and watches the duel. Mace knocks Palpatine's lightsaber from his hand , smashing the window of the Chancellor's Office, and Palpatine falls to the ground. At this point Palpatine asks Anakin for help, saying he was right about the Jedi wanting to depose him and take over ( it is unclear whether the Sith Lord is playing weak and old at this point, to draw Anakin to his aid). As Mace tells the Sith Lord he has failed, Palpatine blasts Force lightning at the Jedi Master but Mace deflects it back onto Palpatine with his lightsaber, distorting his face.
Anakin demands that Mace gives Palpatine up for trial but Mace refuses, saying that the Sith Lord controls the courts and must be killed. Palpatine begs for Anakin's help, saying only he can save the one Anakin loves, and just as Mace is about to finish Palpatine, Anakin cuts off Mace's hand. Mace is caught off guard and is hit by a resurgence of Palpatine's Force lightning. He is flung out the window and falls hundreds of stories to his death.
Anakin is distraught with what he has done, and confides in Palpatine. Palpatine takes Anakin as his Sith apprentice. Anakin kneels before Palpatine, saying he will do whatever he asks so long as the Sith Lord helps him save his wife. Palpatine bestows upon him the Sith name .Darth Vader..
Darth Sidious gives the order to all Clone troopers of the Army of the Republic around the galaxy to execute Order 66; while Vader is given his first assignment: the destruction of the Jedi Temple . the Great Jedi Purge, which marks the early beginnings of the Galactic Civil War. Across the Galaxy, the Clone Stormtroopers turn against their Jedi masters. Ki-Adi-Mundi gets killed by his troops. Aayla Secura gets shot in the back by Bly. Plo Koon's Jedi Starfighter gets shot down. Stass Allie dies when her speeder bike explodes. On Utapau Obi-Wan barely survives while the Clone Troopers who attempt to assassinate Yoda on Kashyyyk find themselves decapitated by the powerful Jedi Master.
At night, Anakin now Darth Vader marches to the Jedi Temple with a battalion of Clone Stormtroopers. He moves through the temple, striking down all the Jedi he comes across, including the younglings.
Later, Anakin/Vader goes to Padme, who sees the smoke rising from the Jedi Temple but does not know what is happening. He tells her the Jedi have tried to take over the Republic, and there are traitors in the Senate. He tells her that he will go to the Mustafar system, where the Separatist Council has gathered after evacuating Utapau, and he will end the war.
Bail Organa, one of the few senators who has resisted Palpatine's influence over the Galactic Senate, rescues both Obi-Wan and Yoda. He drops them off at the Jedi Temple before heading to the Senate where Palpatine tells them of the .plot of the Jedi to overthrow the Senate.. Amidst thunderous applause, he announces that the Republic will be reorganized as the first Galactic Empire.
The two Jedi Masters go to the Jedi Temple, where the Clone Stormtroopers find themselves no match for Yoda's mastery of the force and his lightsaber skills. They walk past the carnage in the Temple, including a group of young Padawans cut down by a lightsaber. They dismantle a signal calling for all remaining Jedi to return to the Temple and reconfigure it to warn all Jedi to keep away. At the Temple's control center, Obi-Wan looks into the security recordings. In disbelief, he sees Anakin/Vader slaughtering the Jedi (including Younglings) and then kneeling down to Darth Sidious. Yoda says they have no choice but to destroy the Sith . and Darth Vader. Obi-Wan still cares for him and offers to instead (attempt to) dispatch the emperor, however Yoda tells him he is not a match for the Sith's dark powers and he (Yoda) will deal with him.
On Mustafar, Vader slaughters the Separatist Council in cold blood.
Obi-Wan goes to Padme's apartment, looking for Anakin/Vader. He meets Padme and tells her that he has turned to the dark side and killed the younglings in the Jedi Temple. Padme realizes what Obi-Wan intends to do and will not reveal where Anakin has gone, as he is her husband and the father of her child. Obi-Wan deduces this without Padme telling him, apologizes, and leaves.
Later, Padme leaves Coruscant in her Naboo Skiff, departing to Mustafar to see Anakin/Vader. Unbeknownst to her, Obi-Wan secretly boards the ship just before it takes off.
The Naboo Skiff lands on Mustafar. Anakin/Vader and Padme embrace. He tells Padme a lie that he "has brought peace to the Republic, and he can overthrow Palpatine so he and Padme can rule the galaxy together." Horrified, Padme realises that Obi-Wan's story was true. Padme tells him he is going down a path she cannot follow.
Vader sees Obi-Wan emerge from the Naboo Skiff. Now evil and enraged, after calling Padme a "liar", he uses the Force to choke her, thinking she led him there. She loses consciousness and Vader releases his grip on her. Obi-Wan and Vader break out into a ferocious, lengthy lightsaber duel.
In the Senate building, Yoda confronts Darth Sidious, finally recognizing him as more then just a leader in the Senate. The Sith Lord blasts the diminutive Jedi Master with force lightning but Yoda recovers and force throws Sidious across the room. Sidious attempts to flee but Yoda blocks his path and they engage in a fast and furious lightsaber battle, bringing them to the deserted main area of the Senate chamber.
Yoda and Sidious then undertake a force battle, hurling senate pods at each other, before the Sith Lord once more engages Yoda with force lightning. In a battle of wills an explosion of force powers occurs, blasting them apart, Sidious barely clinging to the senate pod while Yoda falls to the floor. With Bail Organa's help, Yoda manages to escape.
The epic lightsaber duel between Obi-Wan and Darth Vader brings them to many locations on Mustafar, crossing lava on a small platform. Eventually, Obi-Wan gains the high ground and clinches the battle due to favourable positioning. They both know Obi-Wan has the upper hand, and Obi-Wan pleads his former Padawan not to advance saying "It's over Anakin. I have the high ground." (A metaphorical reference to a moral high ground). Despite this, Vader arrogantly ignores his disadvantageous stance and charges at Obi-Wan, who in the blink of an eye cuts off both of Vader's legs at the knees, as well as his left arm. Vader tumbles down the embankment and rolls to a stop at the edge of the lava. Obi-Wan tells him that he was like a brother to him and that he loved him, and that he was the chosen one, the one who was destined to destroy the Sith, not join them. Vader's proximity to the molten river causes the him to burst into flames, his lasts words to Obi-Wan before bursting into flames are, "I HATE YOU!". He suffers massive, scarring burns that mangle his physical features.
Obi-Wan takes Vader's lightsaber (which he will give to Luke in Star Wars Episode IV: A New Hope) and leaves with the badly-injured Padme and the droids on the Naboo Skiff.
Darth Sidious arrives at Mustafar with a squad of Clone Stormtroopers. They rescue Darth Vader from the edge of death.
Obi-Wan arrives at Polis Massa and Padme is brought to medical assistance. She is dying, not from bad health but from a lack of will to live. They work to save her babies.she has twins. A boy and a girl are born. While dying, Padme gives them the names .Luke. and .Leia..
Occurring simultaneously with the birth of his children, Vader is given a special suit. On Coruscant, at a secret Reconstruction Lab, Vader is given a new artificial body (which includes new legs and a new arm). He is dressed in black armor, a face mask is sealed tightly, and his helmet is fitted. He begins to breathe like a horse.
With Padme's last breath, she says there is still good in Anakin/Vader. Padme Amidala Skywalker dies.
Darth Vader regains consciousness. He asks what happened to Padme. Darth Sidious tells him "It seems, in your anger, you killed her." Furious with grief, Vader unleashes a massive scream and unleashes his Force powers in a rage that distorts and destroys the droids in the room.
On the Tantive IV blockade runner, Obi-Wan, Yoda, and Bail Organa sit at a conference table. They agree to keep the children safe and hidden. 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 will be sent to his father's stepfamily 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 Antilles of the Tantive IV. He orders a memory wipe of the protocol droid.
On Naboo, Padme's funeral takes place in a solemn ceremony. Her recent pregnancy is still evident, however this was by design so that it appeared that she and, more importantly, any babies she was carrying died before she gave birth. The funeral was therefore not only for Padme but also for her unborn child (the second child having only been discovered in secret by Obi-Wan, Yoda and Bail Organa).
Yoda goes into hiding to begin his self-imposed exile.
On the bridge of a Star Destroyer, Emperor Palpatine and Governor Tarkin are joined by Darth Vader, watching what looks like the beginning of the construction of the first Death Star or its prototype.
On Alderaan, the infant Leia is brought by Bail Organa to his wife, the Queen of Alderaan. She takes her and rocks her.
On Tatooine, Obi-Wan brings the baby Luke Skywalker to his new family: Owen and Beru Lars, his step-uncle and aunt. They look out to the horizon and watch the setting of Tatooine's twin suns.