As Episode II begins, we learn that Amidala has left the throne on Naboo and has been replaced by the newly elected Queen Jamilla. Now going by the name Padme Naberrie, she represents Naboo in the Galactic Senate. At one point, Senator Padme intercedes in a dispute between the Geonosians, the Kaminoans, the Commerce Guild, and the Intergalactic Bank Clan. She uncovers some corruption (created by Darth Sidious) and possible plans by the Neimodians to re-arm themselves. She voices this concern in the Senate.

However, after doing this, bounty hunter Zam Wesell attempts to assassinate Padme. Now a Jedi Master, Obi-Wan and Anakin prevent this from happening and chase Zam down at a club on Coruscant called Dexter's Diner. There, they attempt to interrogate the bounty hunter, but she is killed by a Kyber Dart shot from Jango Fett. Fett was hiding in the shadows and gets away.

At this point, the Jedi Council assigns Anakin Skywalker to accompany Padme back to Naboo where she'll be safe. He takes her back to the planet and meets her parents, Jobal Naberrie and Ruwee Naberrie, as well as her sisters. Jar Jar and the other Gungans come along and also vow to protect Padme.

Meanwhile, Obi-Wan goes on a quest with Plo Koon to find out more about who is behind the assassination attempt and the corruption in the Senate. He travels to a planet run by Count Dooku and discovers plans for a clone army to be created. He also tracks down Jango Fett and his young son Boba Fett. Turns out that Jango is being used as a template to make the clones. At one point, Plo Koon is killed by Jango. Jango and Obi-Wan have a deadly battle in the rain at a landing platform, but Jango and son get away in the ship Slave I.

Back on Naboo, Anakin has a vision of the future and sees his mother in great danger. At the same time, a second assasination attempt takes place on Padme. Anakin decides to take Padme into hiding back on Tatooine and find his mother. When they arrive, Anakin interrogates Watto and discovers that his mother has married Cliegg Lars. They live on the Lars Homestead (seen in A New Hope) and Anakin is rediscovers C-3PO with his mother. He now has a step-brother, Owen Lars. Anakin speaks with him about the attempts on Padme's life and they try to discern what will happen next.

On the other side of the galaxy, Obi-Wan tracks down Jango and Count Dooku to a planet run by Poggle the Lesser, and alien who specializes in creating battledroids for the Trade Federation. Poggle has had created a bunch of new super battle droids as well as the traditional Destroyer Droids and battledroids. They are also preparing to create a clone army of Clone Troopers (who later become Stormtroopers). Obi-Wan alerts the Jedi Council and an army isdispatched.

At the same time on Tatooine, Padme is attacked and kidnapped. She is taken to the same planet that Obi-Wan is on. Anakin is unsure if he can save her,but chases after her.

Mace Windu and the Jedi arrive on the planet and have a fierce battle in an arena with the droids, Jango, and a beast called the Reek. Windu kills Jango in the battle, thus sparking Boba Fett's hate for the Jedi.

Anakin is nowhere to be found, and even Yoda engages in the fight. After Anakin finally does arrive he attempts to save Padme, but fails. Obi-Wan insists she is dead, but Anakin doesn't believe a word of it. A lightsaber battle soon erupts between Obi-Wan, Windu, Anakin, Count Dooku (revealed to be Lord Tyranus), and another dark Jedi. The battle rages on, and soon Anakin believes that the only way he can save Padme is by turning to the Dark Side, despite the warnings of Obi-Wan. He turns on his master, thus leading to Episode III. Source -www.theforce.net

However, another trawl around the web has brought forth another account of how the Episode II plot pans out. See below...

Episode II's opening scroll describes an interplanetary movement, led by former Jedi Count Dooku, to secede from the Republic. Amidala, now the senator of Naboo, travels to Coruscant to take part in an important vote on whether the Republic should create an army to fight Count Dooku's acolytes. As her spacecraft enters a docking bay, a bomb detonates and kills the senator's body double.

After the real Amidala arrives in the Senate's chambers, Chancellor Palpatine and a few senators, including Bail Organa and Jar Jar Binks, meet to discuss the idea of creating a clone army for the Republic. The legislature later reconvenes and votes in favor of amassing troops.

After the vote, there is another assassination attempt on Amidala. Anakin Skywalker and Obi-Wan Kenobi, who had been summoned by the Naboo senator earlier, follow the perpertrator in a high-speed chase through the streets of Coruscant. Just as they're about to capture the would-be assassin, she's herself killed by a mysterious dart. Obi-Wan later learns that the weapon was produced on a world called Kamino.

The Jedi Council dispatches Obi-Wan to Kamino while Anakin is told to remain with Amidala for her protection.

Meanwhile, Darth Sidious warns Count Dooku that a jedi is on his way to Kamino. Dooku, also known by the Dark Side moniker Darth Tyranus, sends his lackey Jango Fett to keep an eye on Obi-Wan. As Anakin and Amidala grow closer on Naboo, Obi-Wan arrives on Kamino. The planet's alien prime minister tells Kenobi that Kamino is producing an army of clones for the Republic, a task which he claims was ordered by the Jedi Council.

While studying the cloning facilities on Kamino, Obi-Wan is attacked by Jango Fett. The two square off in a hangar bay amid pouring rain. Fett manages to subdue the Jedi long enough to make his escape. Back on Naboo, Anakin dreams that his mother is in mortal danger. He convinces Amidala to travel with him to Tatooine, disobeying the Jedi Council's orders that they remain in the safe haven of Naboo. On the trip to Tatooine, the budding passion between Anakin and Amidala is consumated with a kiss. As Anakin and Amidala head to his homeworld, Obi-Wan tracks Jango Fett's spacecraft to the Geonosis system. Fett tries to dodge the Jedi by flying into an asteroid belt. In a chase sequence reminiscent of The Empire Strikes Back, the bounty hunter eludes Obi-Wan once again. When the latter emerges from the asteroid field, he notices two Trade Federation 'droid ships circling Geonosis. Upon arriving on the rocky world and observing the native alien race building what appear to be "super battle droids," Obi-Wan reports his findings to Chancellor Palpatine. A Jedi army is dispatched, but not before Darth Sidious warns Count Dooku, who is headquartered on Geonosis, of the eminent attack. Obi-Wan is captured by Dooku's forces shortly thereafter.

On Tatooine, Anakin and Amidala learn that Shmi Skywalker married a man named Cliegg Lars and moved onto his farm outside Mos Eisley. Upon arriving at the farm, they're told that Shmi has been missing for several hours. An agitated Anakin goes looking for his mother, but when he tracks her down it already is too late. Shmi, captured and beaten by Sand People, dies in her son's arms.

After spending the night by his mother's corpse, blaming himself for her death, Anakin buries her. When the morning dawns, Anakin sees a family of Sand People in the distance, walking beneath the same blazing twin suns that Luke Skywalker gazes at in the original Star Wars film. As the apprentice approaches the mother and her children, he ignites his lightsaber. The scene cuts away, leaving the audience to infer the horrific action that follows.

Upon returning to the Lars farm, Anakin sees that Amidala has completed the construction of C-3PO. Anakin recieves a message from Obi-Wan shortly thereafter urging him to come to Geonosis at once. Episode II culminates in a raging third act battle sequence involving the Jedi army, Count Dooku's super battle droids and the clone warriors. Mace Windu squares off against Jango Fett while Obi-Wan and Anakin engage in a lightsaber showdown with Darth Tyranus. When the dust settles, it's unclear who really won the conflict. The only certainty is that the Clone Wars have begun.