Ten years after the Invasion of Naboo, Padme Amidala became Senator of the Galactic Republic with Sheev Palpatine as Supreme Chancellor. A separatist army is growing outside of Coruscant that are unhappy of the Senate. As Padme arrived at Coruscant, she survived a deadly assassination attempt.
Chancellor Palpatine gave the idea of having the Jedi protect Padme from potential danger. Obi-Wan Kenobi is a Jedi Knight and Anakin Skywalker is his Padawan.
At nighttime, a person named Zam Wessel sent in two bugs into Padme's room. The Jedi found and destroyed the bugs. They were able to track Zam throughout the cities with a speeder. As they found her at a nightclub, the Jedi wanted to know who hired her. Before she could answer, she was killed by a toxic dart from a bounty hunter.
Because of the assassination attempts, Anakin decided to take Padme back home at Naboo. At the Jedi Temple, Obi-Wan scanned the toxic dart's origins from a planet known as Kamino. Obi-Wan talked to Yoda and a group of younglings where Kamino is. One of the younglings explained that the data for Kamino was erased from the archives.
At Naboo, Anakin and Padme were having a romantic experience until Anakin heard his mother's cries for help in his sleep. He wanted to go back to Tatooine and save his mother.
At Kamino, Obi-Wan met Lama Su who owns a cloning facility. A Jedi Master authorized a clone army for the Republic but he died before it was fully made. The clones have altered genes that make them reach adulthood at a faster state. Obi-Wan learned that the genetic template is from Jango Fett, a famed bounty hunter. Jango has an unaltered clone or "son" named Boba. Jango Fett learned that Obi-Wan is at Kamino and attacked him with his blaster and jetpack. As the battle ended, Obi-Wan planted a tracking device at Jango's ship, Slave I.
In Tatooine, Anakin and Padme reunited with Watto and Threepio. Anakin traveled through the deserts to a Tusken Raider camp and found his wounded mother. As she died, he slaughtered the entire camp of Tusken Raiders. At Coruscant, Yoda felt Anakin's hatred and pain.
Obi-Wan followed Jango to Geonosis where the Separatists are building a droid army. He tried to contact Anakin but the signal is too weak.
Anakin and Padme returned to Coruscant and they received the message. This gave them an idea to find Obi-Wan. Obi-Wan was captured by the leader of the Separatists, Count Dooku. Dooku told Obi-Wan that the Supreme Chancellor is secretly Darth Sidious, which Obi-Wan didn't believe. Dooku offered Obi-Wan to destroy the Sith, but the Jedi refused the offer.
As Anakin and Padme entered Geonosis, they and Obi-Wan were sent to a coliseum filled with creatures. The three of them were freed from their own restraints. Suddenly, the Jedi Council including Mace Windu helped destroy the droid army and corner Count Dooku. The Jedi became outnumbered by the army. Yoda and the Clone Troopers arrived to help with a Republic Carrier. Anakin and Obi-Wan took a ride with Yoda to follow Dooku's shuttle.
At Dooku's temple, Anakin and Obi-Wan were overwhelmed by his Force lightning. Yoda helped them with his trusty lightsaber skills but Dooku got away.
At the Jedi Council, Yoda told Anakin and Obi-Wan that the Battle of Geonosis is only the beginning of the Clone Wars, with Count Dooku and the Separatists still at large.