Jedi Anakin Skywalker is now 19 years old and still Obi-Wan Kenobi's padawan. He has learned much under Obi-Wan's tutelage but often resents his master's tight constraints and endless criticism. Considering Anakin to be impatient and reckless, Obi-Wan is sometimes patronizing and condescending towards his young apprentice, although he loves him like a brother.
Throughout the galaxy, a separatist movement led by Count Dooku, a former Jedi Knight, is growing. Several thousand solar systems have threatened to secede from the Republic, and Jedi Knights are overwhelmed maintaining peace and order. Senator Amidala (Padme), the former Queen of Naboo, has arrived on Coruscant to vote on the issue of creating a Republic army to assist the Jedi. An assassination attempt is made on her life, killing her decoy. Padme resists any special protection, but when Obi-Wan and Anakin are assigned as her bodyguards, she's pleased to see her old friends.
After a second assassination attempt on Padme, Obi-Wan and Anakin chase and catch the assassin, but she's killed by a toxic dart before they can question her. Obi-Wan visits his old friend, Dex and shows him the dart. Dex tells him it comes from Kamino, a planet of cloners. Obi-Wan consults the Jedi star system databank for Kamino's coordinates but all reference to it has been erased. Yoda and Obi-Wan detect a gravitational anomaly in the star map and determine it must be Kamino's location. Knowing that only a Jedi could delete information from the archives, they can only wonder who and why.
Anakin is given his first Jedi assignment. He is to protect and escort Padme to Naboo where she'll be safer. Jar Jar Binks is appointed as her representative in the senate. Obi-Wan tells Master Yoda and Mace Windu that Anakin isn't ready for the assignment and has grown arrogant, but they insist. Mindful that Anakin may be the Chosen One destined to return balance to the Force, they consider his situation carefully. Conflicted and angry, Anakin feels Obi-Wan has held him back and finds sympathy and encouragement from Chancellor Palpatine who flatters him as being the most gifted Jedi he's ever seen.
Obi-Wan discovers a huge clone factory on Kamino. The Kaminoins warmly welcome the Jedi mistakenly believing he's come to check on the progress of the clone army they say is for the Republic. Obi-Wan learns the clones were ordered by Sifo-Dyas, a Master Jedi Knight killed ten years ago. (Sifo-Dyas, a dissatisfied Jedi, was manipulated by a Sith Lord and placed the order on the Sith's behalf. He was then killed.) Bounty hunter Jango Fett was hired as the DNA donor. As part of his payment, he was given an unaltered clone ‘son, ' he named Boba. Obi-Wan asks if Jango knew Sifo-Dyas, but he says someone named Tyranus recruited him. Obi-Wan transmits a message to Yoda and Mace Windu reporting on the clone army and that Jango is the assassin they are looking for. Blinded to the army's existence, Yoda and Mace-Windu realise the Jedi's power to use the Force has diminished. Obi-Wan attempts to capture Jango, but he and Boba escape. Before they take off, Obi-Wan attaches a tracking device to the ship's hull. He follows Jango to the planet Geonosis and learns the Separatists are building a massive droid army there.
On Naboo, Anakin and Padme are alone together for the first time. Anakin's been in love with Padme since they met ten years before, but she only sees the little boy she once knew. Gradually her feelings deepen, but she's unwilling for Anakin to risk his future as a Jedi. Recently, Anakin has experienced disturbing dreams about his mother. Determined to find her, Anakin goes to Tatooine. Padme accompanies him. Seeking out his former master, Anakin learns his mother, Shmi was sold to farmer Cliegg Lars who freed and married her. At the Lars' farm, Anakin learns Shmi was captured by Tusken Raiders a month before and is believed dead. He finds the Tusken's camp, but Shmi is barely alive. Only briefly can she look upon her son and speak a few words before she dies. Driven by grief and rage Anakin slaughters the Tuskens, including the women and children. From afar, Yoda senses a deep disturbance in the Force.
Before departing Tatooine, Anakin intercepts and forwards a recorded message to the Jedi Council from Obi-Wan on Geonosis, but the message is cut off when Obi-Wan falls under attack. Anakin and Padme go to Geonosis. Mace Windu and a group of Jedi also go to Geonosis to help Obi-Wan while Yoda heads to Kamino to investigate the clone army.