After his city is invaded and a friend killed by Clu's soldiers, a young program named Beck takes the name of "Tron" and, aided by the real Tron, fights back.

As Tron trains Beck, Beck begins to doubt that he can be the next Tron. While trying to evade security, Beck lands in a prison transport and is taken to the games. Meanwhile, Zed falls for a female named Perl and brings her to the garage to show her his work, where she steals Able's classic ENCOM 786.

When Beck and Cutler are thrown into a deathmatch, Cutler forfeits and Beck has to return as the Renegade to rescue him.

Beck is sent by Tron to destroy an Occupation-manned energy drill causing power blackouts in Argon City before its destructive power destabilizes the Grid.

When Beck's identity disc is stolen on the Light Rail, his memory begins to unravel. Hoping to prevent permanent memory loss or identification as the Renegade, he and Tron go to Purgos, Argon City's closest neighbor, to recover it.

After stealing a valuable data cube from General Tesler's ship, Beck (as the Renegade) is chased by Paige over the Sea of Simulation. When they crash on a destabilized island, Paige reflects on the events that led her to becoming a soldier of the Occupation.

Beck intercepts a disk modification that enhances the physical abilities of any program who wears it, but it has some unfortunate side effects.

When General Tesler offers a reward, as well as the lifting of Argon City's curfew, for the capture of the Renegade, programs all over Argon City began to falsely accuse each other.

Dyson, once Tron's lieutenant and now high-ranking in Clu's takeover, comes to Argon City to check up on Tessler.

Beck seeks to stop Tron from killing Dyson.

A furious Tesler publicly challenges the Renegade to appear in Argon Square and surrender himself, promising to free additional prisoners and end the curfew if he does so. Beck accepts the challenge and narrowly escapes capture. Able later reveals that he knows that Beck is the Renegade.

Able heads to the Outlands to confront Tron over his use of Beck as the Renegade, leaving Mara in charge of the garage.

On a trip to Gallium City through a storm, Beck discovers a one-way portal. He also learns that he wasn't the first program that Tron had trained as a renegade.

The Renegade recruits three programs who caught his attention by tagging the grid with the message, "Tron Lives." He discovers one of them is Mara.

Tesler uses a mind-control agent to build an army. When Mara falls victim to it, Zed and the Renegade work together to help rescue her.

Beck tries to rescue a fleeing government scientist before Paige and the Occupation finds her; Paige and Beck become passengers on the same runaway train and Beck must save the innocent programs on the train without revealing his identity.

Beck and Paige go out on a date, and Paige begins to see Beck's views. Meanwhile, Pavel tests the augmentation boost, but Paige catches him, misconstruing Beck's advice. Tired of her interference, Pavel plots to get rid of Paige once and for all, while Beck decides that an appearance by the Renegade may finally win Paige over.

Cyrus, seeking revenge on Beck and Tron, impersonates the Renegade and kills an innocent program. With the city against him, Beck is forced to make the difficult choice of saving Tron or his friends.

Tron tells Beck that he is dying and that the only way to stop his illness is to use the Occupation's new super recognizer.