Dealing with similar concepts to other incarnations of Ghost in the Shell, the game has an original storyline which follows on from and refers to the PlayStation 2 game's plotline.

Tron: Evolution serves as a precursor to the movie Tron: Legacy and sequel to both the graphic novel Tron: Betrayal and the Nintendo Wii and DS versions, Tron: Evolution - Battle Grids. It is designed to be an integral part of the Tron story, featuring certain characters and settings from both films. Evolution explains the events that led to Kevin Flynn's imprisonment inside the Grid,[1] as well as telling how the Grid evolved through the years. The player controls a Monitor program named Anon (short for anonymous), a security program written by Flynn to investigate a conspiracy in the world of Tron.