However, Qui-Gon is the mentor and master of Obi-Wan Kenobi, a young padawan or jedi apprentice with a pivotal role of upcoming events on the universe. Both are in charge by appointment of the Supreme Chancellor Valorum to discuss with the Trade Federation the ending of a blockade to the small planet of Naboo.

  The Trade Federation is hardly willing to negotiate anything, so the two jedi are forced to take matters on their own and travel to the planet to warn the young Queen of the upcoming invasion of the planet. After a confrontation, the queen, the jedi and a few scorts leave the planet of Naboo toward Coruscant, in search of help and support on the Galactic Senate. But a malfunction on the ship, made the group to stop in the remote planet of Tatooine.

  There Qui-Gonn will meet a young and charismatic kid known as Anakin Skywalker, the boy is an skilled mechanic and podracer, and decide to help the group to repair the ship, but for Qui-Gon the boy is also gifted in the skills of the Force and for him is the fulfillment of an old ancient prophecy of a boy who "will bring balance to the Force".

  Qui-Gonn decide to take young Anakin as his new apprentice, considering the fact that his last pupil, Obi-Wan is more than ready to face the trials of the jedi council. When Anakin is tested by the elders of the council his affinity with the Force is tested but also a clouded future is revealed. According to Yoda, Anakin has much fear inside, which could lead to the dark side.

  Qui-Gonn's plans for Anakin are abruptely interrupted by the situation on Naboo and when the queen decide to return to the planet, the group, advised by the council, decide to protect Queen Amidala. Taking Anakin with them to Naboo, when a war is beginning to arise, the young boy finds himself, all of the sudden in the middle of a space battle. There Anakin knocks down the main generator of the Trade Federation Battle Station, making useless any effort of conquering the planets by the army of battle droids, whom without the station are helpless.

  However, on the Theed palace, Qui-Gonn and Obi-Wan are dueling with a deadly enemy on the figure of a young sith apprentice, Darth Maul. Darth Maul with his double blade lightsaber prove to be a worthy opponent for the two jedi. On this fight, Qui-Gonn loses his life, but after the dark apprentice is struck down by Kenobi, a dying Qui-Gonn ask for Kenobi to promise him that the boy will be trained on the ways of the Force. Kenobi accepts the request of his dying master and takes the boy as his Padawan learner. Later, the jedi council decides to approve Obi-Wan's decision.