In 1989, seven years after the events of the first film, Kevin Flynn, who has been recently promoted CEO of ENCOM International, disappears. Twenty years later, his son Sam, now ENCOM’s primary shareholder, takes little interest in the company beyond playing an annual prank on its board of directors.
After being freed from police custody for speeding on his motorcycle to ENCOM Headquarters, Alan Bradley, an ENCOM executive and friend to Sam’s father, asks Sam to investigate a strange pager message originating from his father’s shuttered video arcade. Sam discovers a large computer in a hidden basement, which suddenly teleports him to the Grid, a virtual reality created by his father that exists within ENCOM’s computer mainframe. He is quickly captured and sent to “the Games”, where he is forced to fight a masked program named Rinzler. When Sam is injured and begins bleeding, Rinzler realizes that Sam is a human “User” and takes him before Clu, the Grid’s corrupt ruling program who resembles a younger Kevin Flynn. Clu nearly kills Sam in a Light Cycle match, but Sam is rescued by Quorra, an “apprentice” of Flynn, who conveys him to his father’s hideout outside Clu’s territory.
Flynn reveals to Sam that he had been working to create a “perfect” computer system and had appointed Clu and Tron (a security program created by Bradley) its co-creators. During this construction, the trio discovered a species of naturally occurring “isomorphic algorithms” (ISOs) not conceived by Flynn, bearing the potential to resolve various mysteries in science, religion and medicine. Clu, considering them an aberration, betrayed Flynn, seemingly killed Tron, and destroyed the ISOs. Meanwhile, the “I/O portal” permitting travel between the two worlds had closed, leaving Flynn trapped in the system. Now that Clu has gained complete control, he sent the message to Alan in order to lure Sam onto the Grid and reopen the portal for a limited time. As Flynn’s “identity disc” is the master key to the Grid and the only way to traverse the portal, Clu expects Sam to bring Flynn to the portal so he can take Flynn’s disc, go through the portal himself, and impose his idea of perfection on the human world.
Against his father’s wishes, Sam returns to Clu’s territory on Quorra’s tip-off to find Zuse, a program who can provide safe passage to the I/O portal. At the End of Line Club, its owner Castor reveals himself to be Zuse, then betrays Sam to Clu’s guards. In the resulting fight, Flynn rescues his son, but Quorra is injured and Zuse gains possession of Flynn’s disc. Zuse attempts to bargain with Clu for the disc, but Clu simply takes the disc and destroys the club along with Zuse. Flynn and Sam stow away aboard a “solar sailer” transport program, where Flynn restores Quorra and reveals her to be the last surviving ISO.