Ten years after the Trade Federation’s ill-fated invasion of Naboo, the Galactic Republic under Chancellor Palpatine is on the verge of a schism, with many dissatisfied star systems joining a Separatist movement headed by ex-Jedi Count Dooku. Amid concerns that the Jedi lack the numbers to protect the Republic should a conflict develop with these Separatists, the Galactic Senate gathers to debate the issue of creating an official army of the Republic, with former Naboo queen Padmé Amidala - now the Senator of her planet - traveling to Coruscant to discuss the matter.
Soon after landing, Padmé’s ship is hit with explosives in an attempt to kill her, but she survives thanks to her use of a body double. Discussing the matter with Palpatine, Yoda and other members of the Jedi Council afterwards, Padmé suspects Dooku to be behind the attack, but the Jedi are doubtful that a former member of their order could do such a thing, and Palpatine convinces her to accept old acquaintance Obi-Wan Kenobi - now a Jedi Master - as additional security. Obi-Wan arrives to take up the assignment alongside his apprentice, a now nineteen-year old Anakin Skywalker, who turns out to have had quite the crush on Padmé since they first met back on Tatooine, with the feeling being more or less mutual. Shortly after the reunion though, tensions arise between Obi-Wan and Anakin after the latter voices a belief that they were assigned to Padmé to investigate the attempts on her life, rather than merely protecting her from harm as instructed by the Council.
That evening, Anakin and Obi-Wan foil a second attempt on Padmé’s life, and chase the would-be assassin - a Clawdite by the name of Zam Wesell - to a nightclub on Coruscant’s lower levels, where they succeed in capturing her. Under questioning, Wesell admits that she was hired to kill Padmé by a bounty hunter, but she is killed by a toxic dart fired by a figure in silver and blue armor before she can say more. Following the incident, the Jedi Council assign Obi-Wan to find the bounty hunter Wesell spoke of, while tasking Anakin with escorting Padmé back to Naboo to protect her against further assassination attempts. Aware that Padmé won’t want to leave the galactic capital during a major political event, Anakin is sent to talk with Palpatine in the hope that he can get her to do so; as he and Palpatine talk, the Chancellor heaps praise upon Anakin, suggesting he could one day become a more powerful Jedi than Yoda.
Anakin and Padmé fall further for each other on Naboo, but Padmé reluctantly insists that neither of them can act on their feelings; senators aren’t supposed to have extramarital affairs, and Jedi aren’t supposed to have romantic commitments of any kind, period. Elsewhere, Obi-Wan visits an old friend named Dex, who identifies the dart as coming from a planet named Kamino, whose people specialize in creating clones. He tries to look up Kamino within the Jedi archives, but finds no record of the planet’s existence there. Bringing the matter up with Jedi Council head Master Yoda, he gets a solution he’d never considered; someone deleted the data about Kamino from the Jedi archives. Obi-Wan points out that such a thing should be impossible, at least as far as he's aware, but Yoda clarifies; it's impossible for anyone besides a Jedi. Which begs the question; who among the Jedi did it, and why?
Flying to the supposed coordinates of Kamino in a Jedi Starfighter, Obi-Wan discovers the planet does indeed exist, and learns that the Kaminoans have spent the last ten years secretly creating a clone army for the Republic, having supposedly been hired to do so by a Jedi Master named Sifo-Dyas. Obi-Wan of course has no knowledge of Sifo-Dyas doing such a thing, and as far as he knows, Sifo-Dyas has been dead for almost ten years. He goes on to meet the template for the clone troopers, a bounty hunter by the name of Jango Fett, as well as his son Boba, a clone created without the growth acceleration present in the mass-produced clone troopers as additional payment for his services. Obi-Wan correctly deduces Jango to be the bounty hunter Wesell spoke of, and after informing the Jedi Council of his findings on Kamino - and learning that Sifo-Dyas had not been authorized to commission the clone army from the Kaminoans - he attempts to capture him for questioning. Jango is ready for him however, and after a ferocious skirmish with the Jedi Master, he and Boba manage to flee on their starship, ‘’Slave I’’, but not before Obi-Wan manages to throw a tracking device onto the starship’s hull.
Meanwhile, Anakin is haunted by dreams of harm befalling his mother Shmi, whom he was forced to leave behind on Tatooine when he left to become a Jedi ten years ago. He and Padmé return to Tatooine to look for her, and learn that she was sold to a moisture farmer named Cliegg Lars shortly after Anakin left, with Cliegg later freeing and marrying her. Anakin and Padmé travel to the Lars homestead, where they meet Cliegg’s son Owen and Owen’s future wife Beru, as well as C-3PO, the protocol droid built by Anakin as a child. Shmi isn’t there however, with Cliegg revealing that roughly a month ago, Shmi was kidnapped by a group of Tusken Raiders - the often hostile indigenous population of Tatooine - and she is likely dead by now. Anakin takes a speeder into the desert to search for her, and discovers his mother within the raiders’ encampment, but she dies of torture inflicted upon her following her capture moments after he finds and frees her. This sends Anakin into a rage, and he massacres the entirety of the camp, including its women and children. After Shmi is returned to the Lars homestead and given a proper send-off, Anakin expresses resentment at being unable to save her, and resolves to become powerful enough to save people from dying, while also accusing Obi-Wan of holding him back out of jealousy.
Speaking of Obi-Wan, he uses the tracking device he planted on Jango and Boba’s ship to follow them to the planet of Geonosis. Father and son discover his presence and try to kill him within an asteroid field surrounding the planet, but Obi-Wan survives their attempts to do so, and eventually outwits them by jettisoning his starfighter’s spare parts into the path of a homing missile fired at him by Jango, before using the subsequent explosion to hide himself behind an asteroid. As planned, Jango and Boba assume him to be dead and continue on to the planet. Heading on after them, Obi-Wan discovers Geonosis to be housing a huge underground factory complex currently in the process of building a massive army of battle droids, and later spots Dooku walking and talking with one Nute Gunray, still in charge of the Trade Federation despite the whole invasion of Naboo thing. It transpires that Dooku has indeed been trying to have Padmé assassinated as part of a deal with Gunray, who wants revenge on her for Naboo.
As Obi-Wan continues to tail them, he witnesses them meet with a number of mega-rich alien Corrupt Corporate Executives. Listening in on the conversation, Obi-Wan learns that under Dooku’s direction, the group have pooled their resources together to form a droid army capable of overwhelming the Jedi and the Republic. With Anakin and Padmé’s ship acting as a relay, he contacts the Jedi Council to tell them about the droid army and Dooku’s cabal, but is attacked and captured by Dooku's forces mid-message. Assuring Anakin that the rest of the Jedi will deal with Count Dooku, Jedi Council member Mace Windu instructs him to stay on Tatooine to protect Padmé. Fearing the Jedi will take too long to reach Geonosis from Coruscant however, Padmé decides to head there and rescue Obi-Wan herself, with Anakin forced to accompany her in order to carry on protecting her.
Elsewhere on Coruscant, the revelation about the Geonosian droid army throws the government into a panic. Jar Jar Binks - who’s standing in for Padmé in the Galactic Senate - convinces the Republic’s governing body to grant emergency powers to Palpatine, thereby allowing him to command the clone army on behalf of the Republic. Yoda heads to Kamino to check out the clone army for himself, while Mace takes a small army of Jedi to Geonosis in order to try and help Obi-Wan.
Back on Geonosis, the captive Obi-Wan is visited by Dooku, who turns out to be the master of the late Qui-Gon Jinn, Obi-Wan’s master. After some conversation about Obi-Wan’s presence on the planet, Dooku warns him that the Republic and its increasingly corrupt Senate are both unknowingly under the control of a Sith Lord known as Darth Sidious, with the Jedi unaware of this due to the influence of the Force’s dark side. Obi-Wan doesn’t believe it, and Dooku tells him that Gunray had been in league with Sidious back when he invaded Naboo, before claiming the head of the Trade Federation was betrayed by Sidious around that time, after which he went to Dooku for help and revealed everything. The count urges Obi-Wan to join him, claiming they can destroy the Sith together, but Obi-Wan refuses.
Anakin and Padmé later arrive on Geonosis and enter the droid factory, but get attacked by the Geonosians and separated within the factory’s workings before ultimately getting captured. They are sentenced to a public execution within a Geonosian arena, with Dooku, the Fetts and Gunray all in attendance. Before being ferried out into the arena, Anakin and Padmé decide to accept their love for each other and kiss, aware that their lives may be about to end soon.
Within the arena, the new couple are reunited with Obi-Wan, who’s also been lined up for the same fate. The Geonosians drive a trio of captured monsters to kill them, but the three prisoners manage to evade the beasts long enough for Mace and his Jedi to arrive and rescue them. As the Geonosian audience flees, the Jedi are attacked by a large army of battle droids, both the original models and new ones introduced following the Naboo invasion. Jango later joins the battle, but is beheaded by Mace, before the Jedi are overwhelmed and surrounded by the sheer volume of droids arrayed against them. Calling a halt to the attack, Dooku commends the Jedi for their battle ability, claiming it worthy of recognition in their archives.* He offers to spare their lives if they surrender, but Mace refuses, not wanting to provide Dooku and his newfound allies with hostages. Dooku prepares to resume the attack in response, but the surviving Jedi are saved by the arrival of Yoda and the clone army, whose gunships swoop in and ferry them away from the arena.
The clones and droids begin a massive battle on Geonosis. As the clones get the upper hand, Dooku and the rest of his cabal take the chance to escape, Dooku taking with him plans for a certain planet-destroying space station. Obi-Wan, Anakin and Padmé spot Dooku fleeing upon a speeder and pursue him in their gunship, Obi-Wan hoping to capture the count and nip the present conflict in the bud. During the chase, the gunship comes under attack from Geonosian starfighters, with Padmé getting knocked out of it after coming under fire. Though Anakin wants to halt the chase to rescue her - even if it means getting expelled from the Jedi - Obi-Wan convinces him to carry on with the more important duty of stopping Dooku, pointing out that Padmé would do the same in his position. Padmé proceeds to rally other forces to try and reinforce the two Jedi.
Anakin and Obi-Wan meanwhile confront Dooku within a hangar upon the planet. Anakin lets his impulses get the better of him and recklessly charges Dooku, who takes him out of the fight with Force lightning before engaging and defeating Obi-Wan in a lightsaber duel. Anakin manages to recover and attacks Dooku again, putting up a better fight than last time, but still ends up getting his right forearm lopped off for his trouble. Dooku then finds himself confronted by Yoda, his own former master, with the two of them battling one another with the Force and then lightsabers, Yoda calling on hitherto unseen speed and ability to match Dooku. Unable to achieve anything more than a stalemate with his former master, Dooku uses the Force to collapse a large metal pillar towards the wounded Anakin and Obi-Wan, necessitating that Yoda use his own Force powers to keep it from crushing them and allowing the treacherous count to escape in his own starship. Dooku later meets up with Darth Sidious within the industrial region of Coruscant; he is revealed to be none other than Lord Tyranus, Sidious’s new apprentice and another of his co-conspirators. Tyranus tells Sidious of the war that has broken out between the Republic and the Separatists, and Sidious states that everything is proceeding as he has planned.
Following the conclusion of the events on Geonosis - and the start of the "Clone Wars" - Obi-Wan, Mace and Yoda discuss Dooku’s warning about Sidious controlling the Senate. Yoda is skeptical, pointing out that it’s the dark side’s nature to inspire fear and mistrust, but the Jedi nevertheless agree to keep an eye on the Senate. Elsewhere, Chancellor Palpatine observes clone troopers setting off en masse to fight for the Republic at his command, while Anakin and Padmé - the former now sporting a new cybernetic arm - secretly marry on Naboo, with C-3PO and Padmé’s faithful astromech R2-D2 the only witnesses (as well as the couple's wedding gifts to each other).
