Three years after the Battle of Geonosis and subsequent start of the Clone Wars, the Jedi, the Galactic Republic and their clone troopers continue to war with the battle droids of Count Dooku's Separatists, now known as the Confederacy of Independent Systems. During one such engagement of this war, taking place in orbit around the Republic's capital of Coruscant, the Republic's head of state Supreme Chancellor Palpatine is kidnapped by General Grievous, a Kaleesh cyborg and Jedi hunter who commands the Separatist droid armies. In response to this, Anakin Skywalker - now a full Jedi Knight - and his former master Obi-Wan Kenobi take off in Jedi Starfighters to mount a desperate rescue attempt.
After flying their way through the intense battle up in space, the two Jedi find Palpatine onboard Grievous's command ship, before ending up in another fight with Count Dooku. With Anakin having become a lot more powerful and experienced since losing his right arm back on Geonosis, he returns the favor twice over, and then kills the now defenseless Dooku after being goaded into it by Palpatine. The ship later gets terminally damaged by a Republic Cruiser; Grievous manages to escape, while Anakin and the others succeed in safely landing the ship’s remains upon Coruscant.
Following these events and the Chancellor's return, Anakin enjoys a happy reunion with his secret wife, Padmé Amidala, who reveals herself to be pregnant with his child. Anakin is joyous at the news, but is later haunted by a dream of Padmé dying in childbirth, much like how he once dreamt about his mother before discovering her kidnapped and dead at the hands of Tusken Raiders. He goes to Yoda for advice, but the diminutive Jedi Master tells him only that death is a natural part of existence, and he should learn to accept that he will inevitably lose people he cares about. Elsewhere, Grievous informs Darth Sidious of Dooku’s death, with a nonchalant Sidious claiming he will soon have a much younger and more powerful replacement apprentice.
Back on Coruscant, Palpatine arranges for Anakin to be given a seat on the Jedi Council as his personal representative. The Council - Obi-Wan and Mace Windu included - are less than happy about Palpatine meddling in their business in such a manner, but they nevertheless allow Anakin to join their ranks, though they pointedly refuse to make him a Jedi Master. Anakin considers this an insult, and his negativity towards the Council only gets worse when he learns that they want him to spy on Palpatine, whom they’ve come to distrust since the start of the war, in contrast to his own feelings towards the Chancellor. From The Clone Wars…
Some time after this conversation, Palpatine meets with Anakin and informs him that Grievous has been discovered on the planet of Utapau, adding that he would think it unwise of the Jedi Council to not entrust Anakin with capturing him. Aware that they tasked Anakin with spying on him, he goes on to suggest the Jedi as a whole aren’t too different from the majority of politicians or even their mortal enemies in the Sith; eager to acquire power and unwilling to give it up, regardless of what they might use it for. Anakin argues that the Jedi are selfless as opposed to the self-centered Sith, but Palpatine tells him of a deceased Sith Lord known as Darth Plagueis the Wise, who developed a means of using the Force to save others from dying. The existence of such a power intrigues Anakin, who still fears the worst in regards to Padmé, and Palpatine warns him that he won’t be able to learn it through the Jedi.
Anakin later informs the Jedi Council about Grievous being on Utapau. The Council are naturally eager to capture him and bring an end to the Clone Wars, but reject Palpatine’s request that Anakin lead the campaign on Utapau, instead assigning Obi-Wan to the task. Anakin feels unhappy about being left on Coruscant while Obi-Wan puts himself in danger, but nevertheless apologizes to his former master for his earlier behavior before Obi-Wan departs for Utapau, with Obi-Wan assuring him that he’s already a fine Jedi, and may well be made a Jedi Master on his own merits soon enough.
Traveling to Utapau, Obi-Wan discovers Grievous to indeed be hiding out there, and witnesses him sending the members of the Separatist Council to the volcanic planet of Mustafar, ostensibly to keep them safe from Republic forces. He proceeds to reveal himself to Grievous, and after making short work of his droid bodyguards using the Force, takes on the general himself, with Grievous using his four cybernetic arms and lightsabers taken from slain Jedi to combat him. Obi-Wan gradually gets the upper hand, and then his clone troopers emerge to attack Grievous’s droids, prompting Grievous to try and flee.
As Obi-Wan and Grievous’s forces begin their battle, Mace instructs Anakin to inform Palpatine of this development and see how he reacts to the news. Anakin does just that, and during the conversation, Palpatine reveals himself to be Darth Sidious and Plagueis’s apprentice, thereby making him responsible for the Clone Wars and everything that led up to them, including the Trade Federation’s invasion of Naboo. Though tempted to kill him, Anakin leaves with the intent of turning him over to the Jedi Council; Palpatine allows him to leave, but indicates that his knowledge may well be necessary for Anakin to save his beloved wife.
On Utapau, Obi-Wan eventually manages to chase down and kill Grievous. Upon hearing this news, Mace and three other members of the Jedi Council prepare to visit Palpatine in order to make sure he surrenders the emergency powers he’s had since the start of the Clone Wars, whereupon Anakin informs him of Palpatine’s dual identity. Fearing for the Jedi Order’s future whilst Palpatine remains the Supreme Chancellor, Mace decides to make the visit a full-on arrest attempt, while instructing Anakin to wait in the Council Chambers until they resolve things. Anakin initially does so, but later takes a speeder to Palpatine’s office, fearful that the man’s death will deprive him of his only means to save Padmé.
At the office, Mace and his three fellow Council members attempt to detain Palpatine, who responds by drawing a lightsaber of his own and attacking the Jedi, killing all of them bar Mace, who eventually manages to overpower and disarm him moments before Anakin’s arrival. Backed into a corner, Palpatine frames the scene as an attempted Jedi coup to Anakin, before attacking Mace with Force lightning. Mace manages to block and redirect it back at the Chancellor however, deforming his face in the process, and decides to just execute Palpatine right then and there, reasoning that his sway over the Republic makes him too dangerous to leave alive. He raises his lightsaber, only for Anakin - unwilling to let Palpatine die - to draw his own and slice off his hand, with Palpatine killing him right after. Anakin is horrified by his deed, but nevertheless pledges himself to Palpatine’s service and the dark side of the Force, unwilling to lose Padmé. Palpatine assures him that they can discover Plagueis’s power together and accepts him as an apprentice, christening him Darth Vader.
Palpatine and the newly minted Vader agree that the Jedi are a threat to the Republic, and must be dealt with before they can cause any further trouble. Under Palpatine’s instruction, Vader and an army of clone troopers march to the Jedi Temple on Coruscant and massacre everyone inside, from the masters to countless younglings being trained as Jedi, while Palpatine has the clones throughout the galaxy execute Order 66, a secret command for them to turn on and murder the Jedi leading and fighting alongside them.From The Clone Wars… Caught off-guard by these surprise attacks, the Jedi die in their thousands, with Obi-Wan and Yoda - who had been leading a war effort upon the Wookiee homeworld of Kashyyyk - among the handful of survivors. They are later rescued by Bail Organa, a Republic senator with Jedi sympathies who witnessed the attack on the Jedi Temple, with Yoda receiving aid from a Wookiee named Chewbacca beforehand.
With the Jedi seemingly dealt with, Vader informs Padmé of their supposed coup, before traveling to Mustafar and killing the Separatist Council, the cabal and their droids having served their purpose as a boogeyman for Palpatine to unite the Republic against. As this happens, Obi-Wan’s group learns of a broadcast from the Jedi Temple instructing the surviving Jedi to return there. Recognizing this as a trap, Obi-Wan and Yoda resolve to return to the temple and halt the broadcast before it can lure any more Jedi to their deaths. Bail flies them to Coruscant, and he and Padmé later witness Palpatine denouncing the Jedi as traitors to the Galactic Senate, before announcing the reorganization of the Republic into the Galactic Empire.
As democracy and liberty die within the galaxy, Obi-Wan and Yoda infiltrate the decimated Jedi Temple and reconfigure the broadcast to warn the surviving Jedi to stay away. Investigating security footage of the massacre, Obi-Wan discovers - much to his horror - his former apprentice’s role in the deed, as well as Palpatine’s duplicity. Yoda insists the Sith must be destroyed; with Palpatine too powerful for him to take on in a battle, Obi-Wan reluctantly agrees to kill Vader while Yoda deals with his master.
Unsure of where to find Vader, Obi-Wan asks Padmé about his location, while also informing her about his and Palpatine’s betrayal. Unwilling to believe the accusations and fearing for her husband’s life, Padmé says nothing, and Obi-Wan leaves after apologizing and correctly guessing the identity of her child’s father. Wanting to learn the truth for herself, Padmé travels to Mustafar, with Obi-Wan stowing away upon her hardship.
Upon Mustafar, Vader is taken by surprise at Padmé’s arrival. He dismisses Obi-Wan’s allegations as the man trying to turn her against him, but then offers to kill Palpatine so that he and Padmé can rule the galaxy together and remake it as they please, causing a distraught Padmé to realize he truly has turned to the dark side. She tries pleading with him to return to the light, but Obi-Wan chooses that moment to reveal himself to both. Unaware of the reality of the situation, Vader accuses Padmé of conspiring against him with his former master and Force chokes her into unconsciousness.
After Obi-Wan disembarks from the starship, Vader accuses him of turning Padmé against him, to which Obi-Wan retorts that it’s Anakin’s own behavior and attitude that’s responsible for that. Vader dismisses the Jedi as liars and claims he has brought peace, freedom, justice and security to “[his] new empire”, before declaring Obi-Wan an enemy when his former master declares his allegiance to the Republic and democracy. Realizing Vader cannot be reasoned with, Obi-Wan draws his lightsaber, and the two of them begin an epic lightsaber duel.
While the events on Mustafar play out, Yoda confronts Emperor Palpatine within his office in the empty Senate building. The two engage in a battle that eventually moves to the Senate chamber, the pair fighting first with their lightsabers, and then with the Force. At the climax, the Emperor tries to overpower Yoda with his Force lightning, before both are blasted away by the energy from their struggle, with Yoda falling to the chamber floor, defeated. Bail later helps him escape the building, and Yoda resolves to go into exile following his failure to defeat Palpatine.
Back on Mustafar, Obi-Wan and Vader’s duel takes them to a hover platform above the planet’s lava flows, before Obi-Wan jumps off and onto a nearby lava beach. Remembering how he was once in the opposite position of a similar scenario thirteen years ago, Obi-Wan urges Vader to not try and follow his lead, but Vader is too confident in his power to listen. He leaps over his former master, whereupon Obi-Wan takes the opportunity to slice off all his remaining non-cybernetic limbs and send him rolling to the edge of the beach. He laments how Vader went against the prophecy that foretold he would destroy the Sith and bring balance to the Force, to which Vader screams his hatred for his former master. Obi-Wan responds with the admission that he once saw Vader as his brother, before the heat of the nearby lava sets Vader on fire. Unwilling to see his former apprentice suffer, Obi-Wan leaves Mustafar with Padmé, assuming Vader to be dead.
Obi-Wan meets up with Bail and Yoda at a medical facility on the remote planetoid of Polis Massa, where an examination reveals Padmé to be dying as a result of Vader’s actions. She gives birth to a boy and a girl, whom she names Luke and Leia, respectively, and expresses a belief that there is still good in Vader before dying. Around roughly the same time, Palpatine retrieves the still living Vader from Mustafar, and arranges for him to be transformed into a black cyborg. After awakening and learning of Padmé’s fate from Palpatine, Vader destroys his operating room with the Force before letting out a scream of despair, having granted his wife the very fate he’d tried to spare her from, and lost everything else dear to him in the process.
Back on Polis Massa, Obi-Wan, Yoda and Bail agree to hide Vader and Padmé’s children from Palpatine, with Bail adopting Leia as his own daughter, and Obi-Wan electing to take Luke to the planet of Tatooine and watch over him as per Yoda’s suggestion. Before departing to begin his exile, Yoda reveals to Obi-Wan that Qui-Gon Jinn has mastered a technique that allows the dead to communicate with the living from beyond the grave, and encourages him to study it himself. Bail gives the droids C-3PO and R2-D2 - Vader and Padmé’s wedding gifts to one another - to Raymus Antilles, the future captain of the Tantive IV, while instructing him to have C-3PO’s mind wiped.
Padmé is given a grand funeral on Naboo, her preserved body seemingly still pregnant with Luke and Leia. Elsewhere, Vader, Palpatine and a certain Wilhuff Tarkin oversee the construction of the first Death Star, while Obi-Wan brings its future destroyer to Owen and Beru Lars, leaving Luke in their care before departing to take up the life of a hermit in the nearby desert. Still holding baby Luke, Owen and Beru look up towards the horizon and twin suns of Tatooine.
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