ENCOM CEO Kevin Flynn (Jeff Bridges) creates a digital clone of himself called CLU to work alongside Tron in developing a new Grid to hold the digital world. CLU can reformat programs and is programmed to make the Grid perfect.
Eventually, new programs, the ISOs, that are not created by Users and are actually alive, are born. CLU views them as a virus and plans to destroy them, but Kevin and Tron see them as the next step of the digital evolution and attempt to prevent CLU from destroying them. In the process, CLU reformats Tron as his second-in-command, Rizzler, and Kevin is trapped inside the digital world, leaving his 12-year-old son Sam alone.
Kevin has developed a program, contained within a disc, that'd allow programs to leave the digital world and come to the real world. CLU wants the disc in order to use the program to invade Earth alongside his army of reformated programs, destroy the humanity, whom he also views as a virus, and take over the world. However, Kevin manages to stay hidden with the aid of the ISOs.
15 years later, CLU sends a page to Alan Bradley (Bruce Boxleitner) from Flynn's Arcade, planning to lure someone close to Kevin there in order for him to digitalize this person and take him/her as a hostage to force Kevin to come out of hiding and turn in the disc.
Sam, now a rebellious 27-year-old computer expert, decides to investigate the origin of the page and is taken to the digital world, where he is forced by CLU to compet against Rizzler, but is saved by Quorra (Olivia Wilde), a ISO that takes him to Kevin, finally reuniting father and son.
Sam and Quorra slowly fall in love and them and Kevin plan to escape the digital world. However, they must do so before the portal opened by the Laser closes, as Kevin has programmed it to only be capable of being opened from the outside and for a limited period of time in order to prevent CLU from reaching our world.
They are helped by Castor (Michael Sheen), a ISO that runs the End of the Line Club in Tron City, the center of the digital world. However, Castor betrays them by telling CLU their location.
Now, the trio must find a way to reach the access point to the real world while being pursued by CLU, Rizzler and their soldiers.