Able sends Beck to Gallium in order to pick up an order but on the way, he is caught in a traffic jam caused by a Grid storm closing the highway. Instead of waiting it out, Beck rides through the outlands, only to get lost. He discovers a large energy pool and slips into the whirlpool.
He sinks through it into a cave, where all that can be seen is a mirror. While observing his reflection, a shadow crosses his reflection. He steps closer and realizes there is something inside. He goes through and is restrained by a shadowy program.
Back at the garage, Able asks Link if he has seen Beck. Because he has heard no word back, Able becomes somewhat worried that something might have happened to him. Upon entering his office and turning the light on, Able finds Tron who is also looking for Beck. Tron informs him about something sinister happening in Purgos and shows him Able a security clip that was encrypted. The clip shows Dyson, whom Tron plans to send Beck to take down. Able volunteers to go in Beck's place.
Beck awakens in a dark room. A voice far above tells him that he is safe in the voice's home. Beck apologizes for intruding, as the program, who has his circuitry appearing on his face and his entire body, walks down the walls, but the program will not allow Beck to leave. He reveals that he knows Beck's true identity as the renegade. He steps into the light to reveal white circuitry all over his face.
Beck reaches for his disc but the program has confiscated it. The program allows him to have it back and the renegade follows him down many stories.
In armored light vehicles, programs, including a hooded Able, are taken to a factory. In the elevator, the strict rules are given of no communication with the other programs.
Beck goes deeper into the program's "fortress" which was repurposed. He tells Beck of his vendetta against CLU and shows him a device he's been working on.
Able continues to snoop around the factory until he finds Dyson ordering a guard. Dyson surprises him and asks to see his disc. A worker barely saves Able from trouble before Dyson scolds the man to keep his workers in line.
After climbing to the bottom, the program reveals his machine that will free the Grid by first destroying it. It is powered by the storm above them. The machine rises with both programs on it and though Beck fights him, he knows all of Beck's moves. Before falling, Beck is caught by a chair, which restrains him. The unknown program then reveals that, he was the first renegade trained by Tron.
The former renegade claims that it is more than mere coincidence that Beck showed up. The program, reveals that he requires more than one person to escape the prison that he was trapped in. The device spins around as it ascends from the depths, causing Beck to worry.
At the end of the shift at the factory, Able looks over the edge of a deep ravine, until he is interrupted by Dyson. Dyson asks to see his disc now. Red Guards surround him and power up their discs. Able feels trapped until Tron breaks through the door and the two fight off the guards, as Dyson escapes. Able tells Tron that he was unable to find what he was sent to find. That is until, a monstrous yellow Recognizer emerges from beneath them. Able apologizes and says that Tron really needs Beck, but Tron tells him that he needs both Beck and Able.
As the device continues to rise into the stormy sky, Beck begins catching glimpses of an abyss of stars and after he sees CLU in the vision, he finds the strength to escape the restraints. Without him, the device fails. Beck says that fate brought them together so Beck could stop the previous renegade. Beck escapes but the other program falls back into the energy pool and through his prison door, which shatters.
Back in Tron's hideout, Beck apologizes for being late. Tron tells Beck that he is special to Tron. He then reveals circuitry, like that of his predecessor, on his arm.
In the last shot, a hand reaches from the shattered pieces of the prison door.