The Galactic Republic is in turmoil as the greedy Trade Federation sets up a blockade around the planet Naboo in protest of trade legislation. The Supreme Chancellor dispatches two Jedi Knights, Qui-Gon Jinn and his apprentice Obi-Wan Kenobi, as ambassadors to negotiate with the Federation's Viceroy. However, their diplomatic mission quickly goes awry, and the pair are forced to flee the Federation starship with their lives after an assassination attempt. The escape lands them on the surface of Naboo, where they encounter Jar Jar Binks, an outcast from the Gungan society who leads them to his underwater city. The Jedi strike a deal with the Gungans for assistance and make their way to the Naboo's capital to warn Queen Amidala of the invasion by the Trade Federation.

As the situation on Naboo deteriorates, the Jedi manage to rescue Queen Amidala, escaping the besieged planet. Their damaged ship, however, forces them to land on the desert planet of Tatooine for repairs, where they encounter a young slave with an unusually strong connection to the Force, Anakin Skywalker. While Qui-Gon is immediately intrigued by the boy's potential, they are also pursued by a dark and mysterious enemy. Meanwhile, Queen Amidala is desperate to find a way to save her people, leading to a dire decision that will bring them all to the Galactic Capital, Coruscant, where political intrigue threatens to overshadow the growing threat of an unseen and malevolent force.