The conflict that united the people of Naboo and Gungans against the Trade Federation. The Battle of Naboo began when the Trade Federation invaded the peaceful planet of Naboo in order to protest the taxation of trade routes. Queen Amidala escaped and pleaded with the Galactic Senate for aid, but when no help was forthcoming she returned to her homeworld with Jedi Master Qui-Gon Jinn, his apprentice Obi-Wan Kenobi, and Anakin Skywalker. Under the guidance of Jar Jar Binks, Amidala sought out Boss Nass. Together, they overcame long standing prejudices and united against their common enemy.

In order to defeat the Trade Federation, Queen Amidala and her allies devised a bold plan. While the Gungan's distracted the Federations droid army, the Naboo and the Jedi infiltrated the Theed Royal Palace using hidden underground tunnels. In the palace, the Jedi engaged the Sith warrior Darth Maul, who had been sent by his master, Darth Sidious, to ensure that the Trade Federation retained control of the planet. Meanwhile, Queen Amidala, Captain Panaka, and a contingent of Naboo security guards, search for Nute Gunray, the Viceroy of the Trade Federation. While this is going on, members of Naboo's Bravo Flight, under the leadership of Ric Olié, launched an attack against the Federation's droid control ship. Anakin Skywalker, who was hiding in one of the Naboo starfighters, found himself thrust into the space battle as well.

The various battles takes a heavy toll on the freedom fighters, but they ultimately proves victorious. The Gungans fought valiantly before being overwhelmed by battledroids. Darth Maul murdered Qui-Gon Jinn, but was then killed by Obi-Wan Kenobi. Queen Amidala and her entourage captured Nute Gunray. Finally, Anakin Skywalker destroyed the droid control ship, leaving the Federation's droid army helpless.