At the behest of Supreme Chancellor Valorum, Qui-Gon and his Padawan apprentice Obi-Wan Kenobi journeyed to Naboo to settle the trade dispute that threatened the peaceful world. Aboard a Trade Federation battleship, the Jedi were ambushed, but they managed to escape to Naboo's surface.
In the swamplands of Naboo, Qui-Gon rescued a clumsy Gungan outcast, Jar Jar Binks, who swore a life-debt to the Jedi. Qui-Gon's compassionate nature was such that he took the strange alien under his protection. With his help, they journeyed to the city of Theed. There, they freed Queen Amidala and her retinue from the clutches of the Trade Federation, and set off to deliver her safely to Coruscant.
During the trip to the capital, damaged sustained to the Royal Starship forced an unscheduled stop on the Outer Rim world of Tatooine. There, Qui-Gon discovered a young slave boy named Anakin Skywalker, who was strong in the Force. Sensing the boy's potential, Qui-Gon liberated Anakin from slavery. During their departure from Tatooine, Qui-Gon was nearly killed by a dark warrior, whom he suspected to be a Sith Lord.