1989: Kevin Flynn (Jeff Bridges
), now CEO of ENCOM, tells his seven year-old son, Sam (Owen Best
), about his adventures in the Grid, a completely digital world within the Tron computer system that Flynn created. Flynn explains to Sam that, with his counterpart Clu (Jeff Bridges
, body performance; John Reardon
) - the second of a Codified Likeness Utility modeled after Flynn - and the security program Tron (Bruce Boxleitner
), he discovered something amazing within the Grid; a miracle. Sam asks what it is but Flynn holds the story for next time before putting Sam to bed and going to work. A series of newspaper articles and television reports follow announcing the mysterious disappearance of Kevin Flynn after that night. Since the passing of Sam's mother (Amy Esterle
) several years prior, Flynn's absence leaves him effectively orphaned and puts ENCOM's future in a state of jeopardy. Sam is left to stay with his paternal grandparents (Donnelly Rhodes
and Belinda Montgomery
), questioning the nature of his father's disappearance.
20 years later, Sam (Garrett Hedlund
) rides his motorcycle through the night streets towards ENCOM tower. He hacks into the building and evades security cameras as he makes his way upstairs. Meanwhile, a board meeting is being held where Richard Mackey (Jeffrey Nordling
) presents the new OS-12, a secure operating system. When Alan Bradley (Bruce Boxleitner
) inquires about improvements to the system, given the high prices already charged, young Edward Dillinger II (Cillian Murphy
: uncredited) says that the idea of sharing software for free disappeared with Kevin Flynn. Sam breaks into the control room and swaps out the OS-12 master file so that when Mackey attempts to run it, all he sees is a repetitive video of Sam's dog Marv (a Boston terrier). Sam smirks as he passes the boardroom, followed closely by a security guard (Dan Joffre
). When Mackey angrily asks where the master file is, Bradley announces that it's on the web.
The security guard, Ernie, chases Sam onto the rooftops where Sam reveals his true identity as the largest shareholder of the company before he leaps off the edge of the building. He parachutes safely to the ground but gets snagged on a traffic light and is soon arrested by police. Sam makes bail and returns home; a shipping container refitted as an apartment and overlooking the city skyline across the river, including ENCOM tower. Bradley visits Sam, commending him on his latest prank, apparently an annual event that Sam performs on the day of his father's disappearance. Bradley tells Sam that he recently received a page from Flynn's office above his arcade, a number that hasn't been in use for 20 years. Sam reluctantly follows the tip and heads to the arcade. There he finds a secret doorway behind his father's Tron arcade game which leads him down a passage and into a confined control room. Sam sits at the computer to find that it still works and searches through it for information. However, he unknowingly activates a large laser behind him which emits a digitizing ray, sending him straight into the Grid. Shocked at the sudden change in environment, Sam stumbles outside the arcade where he is quickly picked up by a Recognizer. The programs on board restrain him and the Recognizer takes off again.
Sam comes face to face with other captive programs, including one that nervously chatters (Christopher Logan
) and one missing half his face (Kis Yurij
). They are all taken to the edge of the Gaming Grid where they are assigned either for derezzing or games. Sam watches as the nervous program is assigned to the games but, once free, plunges himself into an in-ground fan, derezzing himself. Sent to the armory, Sam's clothes are removed by Sirens (Serinda Swan
, Yaya Alafia
, and Elizabeth Mathis
) and is fitted with armor and an Identity Disc. The last Siren, Gem (Beau Garrett
), instructs Sam to survive before he is led out onto the gaming grid for Disc Wars. He is pitted against an opponent (Allen Jo
: uncredited) whom he manages to defeat before trying to escape the arena. Sam comes out on the final round to face Rinzler (Anis Cheurfa
) who quickly subdues him. When he sees blood on Sam's armor, Rinzler recognizes him as a user and faces him towards a viewing box above the arena where the watching authority figure asks Sam to identify himself. The figure then summons Sam to see him where he reveals himself as a youthful Kevin Flynn. Amazed to see his father, Sam asks if they can go home, but his request is denied. His 'father' then reveals himself as Clu and, after seeing nothing of note on Sam's Disc, sends him to the Lightcycle arena.
Clu's right-hand man, Jarvis (James Frain
), entices the crowd before Sam is put on a team of programs while Clu battles them with his own team. One by one, the racing programs are eliminated while a mysterious figure watches overhead. Before Sam and Clu can face off, the figure intervenes with a Light Runner and blasts a hole out of the arena, escaping off-Grid into the Outlands where other programs' vehicles cannot follow. The figure introduces herself as Quorra (Olivia Wilde
) and takes Sam out to a secluded home situated on a craggy hilltop. Inside, Sam is tearfully reunited with his real father who had been meditating upon Sam's arrival. Quorra shows Sam that Flynn has been teaching her about the real world before they all sit down to dinner. Sam and his father catch up before Flynn answers Sam's biggest question: why he never came home.
Flynn reveals that, as Sam now knows, when he went to work he was really entering the Grid, working with Tron and Clu on creating the 'perfect system'. The 'miracle' that Flynn spoke of before disappearing was the birth of the ISO's; isomorphic algorithms that spontaneously evolved from the Grid without user intervention and with properties that Flynn had never seen before. Their makeup included bio-digital genetics that Flynn was convinced would change the world. However, Clu saw them as imperfections. Tasked by Flynn to create the perfect system, Clu performed a coup, ambushing Flynn and Tron and taking over the system. Tron was presumably derezzed and Flynn was forced to flee into the Outlands while the ISO's were destroyed, an event known as the Purge. The portal - the only way out of the Grid - saw the end of its millicycle window (8 hours in the Grid; just 30 seconds in the real world - which means Flynn's absence of 20 years equated to nearly 20,000 years) and closed on Flynn, leaving him trapped. With Sam's arrival, the portal is open again and Sam argues that they have time to escape, but Flynn refuses. He explains that it's a move that Clu anticipates in hopes of retrieving Flynn's identity disc to use to manipulate the portal. Flynn is also certain that it was Clu who sent the page to Alan.
Understanding Sam's frustration, Quorra goes to him in his room and tells him about a program in the city named Zuse who used to help the ISO's during the Purge and may be of some help. Sam takes Flynn's vintage Lightcycle into the city where he trades it for a cloak. However, he's recognized by the Siren Gem who takes him to Zuse's End of Line Club where a large party is being entertained. There, he meets the eccentric Castor (Michael Sheen
) who promises to take Sam to Zuse.
After finding Sam gone, Flynn resolves to head into the city though Quorra assures him that she sent Sam to someone they could trust. Regardless, they head out as Clu's guards locate Flynn's Lightcycle and trace it to the point of origin. Clu prepares a group and flies out to Flynn's home to find it empty. As he looks around, Clu recalls when he was first created and how Flynn promised that they would change the world together. The thought makes him furious.
Sam, meanwhile, is taken by Castor to a private room above the party while the masked DJ's (Daft Punk
) spin a tune. Castor reveals to Sam that he *is* Zuse but admits that his services have turned with the tide. At that moment, the club is infiltrated by Clu's guards and Sam steps out to fight them. Quorra arrives and fights along Sam but is overpowered and her left arm is derezzed. Flynn then appears and derezzes the rest of the guards before escorting Sam, carrying Quorra who has gone into a state of shock, to the elevator to escape. Zuse propels an extension cord to capture Flynn's Disc as the elevator doors shut and sabotages the lowering mechanism. Flynn manages to slow the elevator before they crash and scolds Sam for 'messing with his Zen thing, man'. They decide to then board a Solar Sailer which should take them directly to the portal.
Clu arrives at the club where Zuse presumes a silent agreement: Flynn's Disc for control of the city. But, as he and Gem watch, Clu orders his guards to rig the place with bombs and, as Clu leaves in his ship, the tower explodes.
As they ride the Solar Sailer, Flynn takes Quorra's Identity Disc and rearranges the corrupted material that will enable her arm to regenerate. He also shows Sam that Quorra is an ISO; the very last one. Her digital readout shows that she has triple-stranded DNA. "Bio-digital jazz, man." Flynn then leaves Quorra with Sam to reboot so that he can 'knock on the sky and listen to the sound'. Quorra wakes up moments later and tells Sam that Flynn saved her during the Purge. They bond further and Quorra asks more about the real world. Sam tries to describe to her what the sun looks like as Flynn looks on, smiling. Suddenly, the Solar Sailer intersects the Rectifier, a large carrier ship. Flynn, Quorra, and Sam hide among the cargo units of the Sailer and discover that programs are encased within, en route to be reprogrammed into an army for Clu. Rinzler then appears and begins to investigate the Sailer. Flynn suddenly recognizes Rinzler as his old friend, Tron; reconfigured as Clu's henchman. Quorra gives Sam her disc and runs into Rinzler's line of sight where she is immediately captured and taken away.
Flynn and Sam use Quorra's distraction to move out. They find Clu giving an announcement to his army. With Flynn's disc in his possession, he intends to use it to allow passage into the real world where they may 'perfect' it. Flynn and Sam agree to a plan and split up. Clu goes to his tower where Flynn's disc is stored. There, Quorra is brought to him and, when he sees that she is an ISO, claims that he has something special in mind for her. Flynn makes his way to the Light Jet hangar where he reprograms a guard, allowing him to access one of the vehicles. Meanwhile, Sam makes his way to Clu's docking tower to rescue Quorra and retrieve Flynn's Disc. He fights off the guards there and intimidates Jarvis, allowing him to retrieve Flynn's Disc. Rinzler confronts him, holding Quorra as a hostage, but Sam fights him off and defeats him by knocking him off the edge of the tower. Sam takes Quorra and leaps off the tower, using a wing-like parachute to glide to the ground. They meet up with Flynn in his Light Jet and Quorra takes the pilot's seat.
Clu storms into the tower to find Rinzler, having climbed back from the ledge, and Jarvis looking sullen. As he watches Flynn's Light Jet leave the carrier, he strikes down Jarvis with his Disc and leaps out of the tower, creating his own Light Jet. Rinzler and a few guards follow. As they fly over the Sea of Simulation, Sam is sent to the Light Jet's turret to fire on their pursuers. Rinzler flies over the Light Jet and he and Flynn make eye contact for the first time. Flynn speaks out to him and the connection allows Rinzler to regain his memories of being Tron. He turns against Clu, crying out "I fight for the users!" However, Clu wins out on the battle, sending Tron sinking into the Sea of Simulation, his armor circuitry changing from red to blue.
Flynn asks Quorra to do something for him just before they arrive at the portal. As they walk up the pathway, they find Clu standing before them. Clu confronts Flynn and insists that all he was trying to do was what Flynn instructed him to. Flynn apologizes to Clu and says that perfection is impossible because it's unknowable; but Clu would not know that because Flynn didn't when he created him. This revelation incites Clu to attack Flynn who yells at Sam and Quorra to continue to the portal. Though determined not to lose his father again, Sam is pushed forward by Quorra. Clu takes Flynn's Disc and reads it to see that it's actually Quorra's; Flynn had swapped his with her before arrival. Infuriated, Clu jumps the gap between the gate and the portal but Flynn performs reintegration; a destructive method of rejoining Clu to him. Flynn watches tearfully and with pride as Sam holds his Disc into the portal. He says, "Goodbye, kiddo" before Clu is merged with him. Sam and Quorra escape the Grid just before the union which results in a massive explosion that destroys it.
Back in his father's office, Sam saves the Tron system onto a microchip that he laces around his neck. He pages Alan to the shop and tells him that he was right about everything. Sam says that he will take back ENCOM and would like Alan as chairman. Leaving the arcade, Sam greets Quorra who asks what they will do now. Sam tells her that he has something to show her and takes her for a ride on his motorcycle. As they ride out into the real world, Quorra sees the sun rise for the first time.