"La amenaza fantasma" desvela la infancia de Darth Vader, el pasado de Obi-Wan Kenobi y el resurgimiento de los Sith, los caballeros Jedi dominados por el Lado Oscuro. La Federación de Comercio ha bloqueado el pequeño planeta de Naboo, gobernado por la joven Reina Amidala, como parte de un plan ideado por Sith Darth Sidious, que manteniéndose en el anonimato dirige a los neimoidianos, que están al mando de la Federación. Amidala es convencida por los Jedis Qui-Gon Jinn y su aprendiz, o padawan, Obi-Wan Kenobi a viajar hasta Coruscant, capital de la República y sede del Consejo Jedi para intentar mediar esta amenaza. Pero esquivando el bloqueo, la nave real resulta dañada, obligando a la tripulación a aterrizar en el desértico y remoto planeta de Tatooine...

The evil Trade Federation, led by Nute Gunray (Carson) is planning to take over the peaceful world of Naboo. Jedi's Qui-Gon Jinn (Neeson) and Obi-Wan Kenobi (McGregor) are sent to confront the leaders. But not everything goes to plan. The two Jedis escape, and along with their new Gungan friend, Jar Jar Binks (Best) head to Naboo to warn Queen Amidala (Portman), but droids have already started to capture Naboo and the Queen is not safe there. Eventually they land on Tatooine, where they become friends with a young boy known as Anakin Skywalker (Lloyd). Qui-Gon is curious about the boy, and sees a bright future for him. The group must now find a way of getting to Coruscant and to finally solve this trade dispute, but there is someone else hiding in the shadows. Are the sith really extinct? Is the Queen who she really says she is? and what's so special about this young boy? All these questions and more in the first chapter of the epic Star Wars saga.