The game begins with the Trade Federation's blockade of the planet Naboo. Jedi Master Qui-Gon Jinn and his apprentice Obi-Wan are assigned by the Jedi Council as part of a mission to officiate the dispute and reach a settlement with the Federation leaders. When they reach the Federation's ship on Naboo, however, they find out that the Federation is not interested in negotiations and is secretly allied with the leader of the Sith, the Jedi Order's enemies; together, they plan to invade Naboo and take control of the galaxy by killing all Jedi. Obi-Wan and Qui-Gon are attacked by Federation droids, but manage to escape. They head to Theed, the capital of Naboo, to warn the unprepared inhabitants about the imminent attack.
During their journey to the city, the two Jedi cross Naboo's swamps and are assaulted by invading troops sent by the Federation. After delivering the warning, they travel to the planet Coruscant to talk with the Jedi Council. They are attacked by more Federation troops after arriving, but the two Jedi are able to defeat them. Jedi Grandmaster Yoda instructs Obi-Wan and Qui-Gon to return to Naboo and help Queen Amidala and her people defeat the Federation. Upon reaching Theed, the Jedi set out to liberate the city. To get around the Federation's droids, they manage to infiltrate the city by going through a secret entrance to the ancient catacombs, but are discovered and forced to battle the droids on their way through.
Obi-Wan and Qui-Gon discover that Amidala has been captured by the Federation and will soon have to sign a treaty handing control to them. Before heading to the Queen's palace to initiate an attack, they free captured citizens on the streets of Theed. The Jedi infiltrate the palace and manage to free the Queen, ruining the Federation's plans. Obi-Wan and Qui-Gon then encounter the Sith apprentice Darth Maul. Qui-Gon is mortally wounded in the battle, but Obi-Wan manages to kill Maul in retaliation. As a result, Obi-Wan's quest to become a Jedi Knight is completed.
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