You start off as Tron and progress to find out about a deadly virus spreading through the ENCOM system. The system's own protection programs (ICPs) see you as the source and attack you. Later on, in a light cycle grid, you meet a friendly program named Mercury (same as in the PC game). Mercury agrees to go after the Corruptor and you agree to go after the virus communication grid (which the User is using to prevent the security system from identifying and neutralizing the virus). You can also start out as Mercury and progress through the game along an alternative storyline.