There were three levels planned and almost finished for the game but cut: The first was a level in the Episode I chapter which has the player playing the scene where Anakin accidently attacks and destroys a Trade Federation ship in the space above Naboo. The second one was for the Episode II levels and featured a playable version of Anakin and Obi-Wan's chase of Zam Weasel in a speeder throughout Coruscant like in the beginning of the movie. The third was the scene in Episode III where Obi-Wan chases General Grevious around Utapau on a Boga creature.

The first level was cut because the developers thought that it bloated its Episode's level count, and they wanted the number of levels between all of them to be mostly even. It is unknown why the Speeder chase was cut, but the Boga chase level was cut due to the developers thinking it clashed with the game's co-op multiplayer feature. Nonetheless, the Trade Federation ship level and the Zam Weasel Chase would eventually be realized in LEGO Star Wars: The Complete Saga. However, the Boga chase level didn't appear in that game at all.