In 1989, Kevin Flynn, the CEO of ENCOM International, vanishes under mysterious circumstances. Twenty years later, his son Sam, who holds a significant share in the company, pulls a prank by making ENCOM’s operating system available for free online. This move is supported by ENCOM executive Alan Bradley, a friend of Flynn, but leads to Sam’s arrest for trespassing. Upon posting bail, Alan informs Sam about a pager message from Flynn’s old, now-closed video arcade, prompting Sam to investigate.

At the arcade, Sam discovers a hidden basement containing a large computer and laser, which digitizes him into the Grid, a virtual reality created by his father. Captured and forced to participate in the Games, Sam encounters Rinzler, a masked program. When Rinzler realizes Sam is human, he takes him to Clu, the corrupt program ruling the Grid who bears a resemblance to a younger Kevin Flynn. Clu’s plan involves using Sam to access the Portal between the Grid and the real world to impose his vision of perfection on humanity.

Flynn, who has been hiding from Clu, explains to Sam that he and his co-creator Tron discovered a race of “isomorphic algorithms” (ISOs) that could solve many natural mysteries. Clu, viewing the ISOs as flawed, betrayed Flynn, killed Tron, and destroyed the ISOs. With the Portal closed, Flynn has been trapped in the Grid. Clu intends to use Sam to retrieve Flynn’s identity disc, which can open the Portal and allow Clu to invade the real world.

Sam, defying his father’s wishes, seeks out Zuse, a program who can help him reach the Portal. At the End of Line Club, Zuse betrays Sam, but Flynn rescues him, although Quorra, an ISO, is injured and Zuse obtains Flynn’s disc. Zuse attempts to trade the disc with Clu but is betrayed and killed. Flynn and Sam escape aboard a Solar Sailer, where Flynn restores Quorra, the last ISO. They are eventually pursued by Clu’s forces, and Flynn sacrifices himself to destroy Clu by merging with his digital duplicate, while Sam and Quorra escape to the real world.

Back in the real world, Sam deactivates the system and plans to take over ENCOM, appointing Alan as chairman. Sam and Quorra, who experiences her first real sunrise, depart together on a motorcycle, leaving behind the digital realm and its perils.