The plot closely follows that of the film, although it expands on some minor events that were not present in the original film, or shows them from a different character's point of view. For example, it follows Queen Amidala (Grey DeLisle) and Captain Panaka's (Jeff Coopwood) journey on Coruscant during Anakin Skywalker's (Jake Lloyd) interview in the Jedi Temple—something that is never shown or mentioned in the film since the film follows Anakin's point of view. It mainly surrounds Jedi Master Qui-Gon Jinn (James Warwick) and his apprentice, Obi-Wan Kenobi (Scott Cleverdon). The story features several boss fights, such as a Tusken Raider Chieftain, Jabba's Pit Beast, and Sith Lord Darth Maul (Gregg Berger).
The Trade Federation, led by Viceroy Nute Gunray, has established a blockade of the planet Naboo amid an intergalactic trade dispute. Hoping to resolve the conflict peacefully, the Chancellor of the Galactic Republic, Finis Valorum, sends two Jedi, master Qui-Gon Jinn and his padawan, Obi-Wan Kenobi, to negotiate with the Viceroy. However, after they arrive on Gunray's ship, the meeting room begins to fill with poisonous gas. Realizing that Gunray plans to assassinate them, the Jedi escape the room and fight their way through the ship, battling the Trade Federation's army of battle droids. They reach the hangar bay and escape in separate ships to the swamps of Naboo.
There, Obi-Wan meets with Jar Jar Binks, an exile of the Gungan city Otoh Gunga, who reunites him with Qui-Gon. Upon travelling to Otoh Gunga, Jar-Jar is imprisoned, leaving Obi-Wan to navigate through the city to rescue him. At the same time, Qui-Gon attempts to negotiate for his release with the Gungan leader Boss Nass. Qui-Gon manages to convince Nass to spare Jar-Jar's life, and they depart for Naboo's capital, Theed, where Obi-Wan is again separated from Qui-Gon and Jar-Jar, forcing him to navigate his way through the Gardens of Theed. Upon doing so, he finds Qui-Gon and Jar-Jar with Queen Amidala and her entourage. He is then required to safely escort the group through the city as an invasion commences. Along with Captain Panaka, they flee the besieged capital and make an emergency landing on the desert planet of Tatooine.
Qui-Gon scours the market of Mos Espa for the vital ship parts needed to escape the planet and encounters child slave Anakin Skywalker, who helps him find the parts in return for help finding components to fix his racer. Following a deal struck with crime lord Jabba the Hutt, in which he had to kill one of Jabba's beasts in exchange for a sum of money, Qui-Gon uses it to make a bet with Anakin's master Watto and wins his freedom.