“life will be better in spring”

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The film opens with a flashback to 1989 as Kevin Flynn - now the CEO of ENCOM - tells his son Sam a story about his adventures in the Grid and about how he, Tron and Clu discovered something amazing and miraculous. Sam asks about it but is told to wait for next time as Kevin leaves for work. It then cuts to a montage of events and news reports about Kevin's disappearance, which has not only jeopardized ENCOM's future, but orphaned Sam.

In the present day, the now-adult Sam breaks into the ENCOM Tower and , despite the efforts of the board - including the son of Ed Dillinger (uncredited Cillian Murphy) steals Encom's new software, releasing it online. After being chased to the top of the tower by a security guard, Sam reveals himself and attempts to freefall off the tower only for his parachute to snag on a traffic light, and he is arrested shortly after freeing himself.

Sam eventually makes bail and returns to his apartment and is met by Alan Bradley, who tells him about a page he received from his Dad's office in the arcade. Reluctantly following the tip, Sam locates a hidden doorway behind the arcade's Tron game which leads him to a secret workshop. He begins searching through his father's computer and unknowingly activites a digitizing ray which transports into the digital world. As the confused young man takes his leave and steps out onto the Grid, he is spotted by a Recognizer, and the programs within assign him to the Games.

He is taken down to the Armoury Sirens, to be clad in armour and given an Identity Disc. Upon arriving in the Disc Wars Arena he narrowly manages to survive and spends his final round battling against Rinzler, who recognizes Sam as a User after seeing him bleed. Clu, who has been watching the events, has Sam brought to his lair. As the two talk, Sam believes he is speaking to his father. However, Clu denies this and has him sent to the Lightcycle arena while a mysterious figure watches them.

Sam is teamed with several other programs in the ensuing race againt Clu and his followers, but ends up as the sole survivor of his group. He is saved from deresolution by the stranger who - while driving away in a Light Runner - introduces herself as Quorra. She takes him to a secret hideaway "off the grid" where Sam is reunited with his father. Over dinner, Kevin answers Sam's biggest question, regarding where he went all those years ago. Kevin relates how he was able to access The Grid, and brought along Tron, as well as Clu to help him create his perfect world. Kevin also reveals that the miracle he mentioned before his disappearance was the birth of ISOs - a brand new form of program created by the Grid itself. However, altercations arose when Clu felt 'imperfections' were rampant on The Grid. Clu then proceeded to take over by ambushing Kevin and Tron. Tron protected Kevin, but was derezzed in the process. Kevin then escaped into seclusion, but also was witness to Clu destroying the ISOs, as he believed they were not part of the perfect plan.

Later, Sam argues with his dad as he believes they can still make their way to the portal - which will remain open for eight Grid-world hours - and return home, but Kevin objects, citing that this is exactly what Clu would want: a prime oppurtunity to steal Kevin's Identity Disc and use the information stored inside to manipulate the portal. Kevin is also certain that it was Clu who sent the page to Alan.

Realzing that Sam is frustrated at being unable to help, Quorra tells him of a program called Zuse who could be of assistance. His mind made up, Sam takes off in Kevin's Lightcycle and keeps guards off his trail by handing the lightcycle away to another program as a distraction. Unfortunately, Clu traces the vehicle's point of origin and investigates Kevin's hideout only to find it empty.

As Sam explores the city he crosses paths with the Armoury Siren known as Gem, who offers to take him to where he needs to go. He accepts and they arrive at the End of Line Club. Gem calls on club owner Castor who reveals himself to be Zuse. However he betrays Sam to Clu and although Quorra and Kevin intervene, Quorra's arm is derezzed in the ensuing brawl, Kevin's disk is stolen as the trio escapes, and the club is ultimately bombed when Clu double-crosses Castor and Gem.

Kevin and Sam continue to argue over what to do next and decide to take a Solar Sailer to the portal. As Kevin reconstructs Quorra's arm he reveals she is in fact the last ISO. As Sam and Kevin bond with each other, Quorra reboots her system and finds out that Kevin saved her.

The trio eventually find the Rectifying Room and realize Clu is making an army by forcibly reprogramming programs to escape into the Real World to "perfect" it. As they try to find their way out, Kevin recognises Rinzler as his old friend Tron, who was not derezzed, but has lost his memories after being reprogrammed by Clu. Quorra then passes the men her disc and distracts Rinzler so that they can track down Clu. Meanwhile Clu has Kevin's disc in place and as he is revealing his grand plan to his army, he is presented with - and insulted by - Quorra. Upon recognizing her as an ISO, Clu dismisses her after mentioning he has something special in mind for her.

After the Flynns contemplate their next move, Kevin seeks transport for them to escape in while Sam makes his way up to Clu's lair and takes Kevin's disk. After a failed attempt to quiz Clu's henchman Jarvis on Quorra's whereabouts, Rinzler returns to the lair with Quorra and engages Sam once again, with Sam emerging victorious after knocking Rinzler off a ledge. Sam and Quorra use a digital wing-like parachute to make their escape and meet up with Kevin in the Light Jet hangar. Clu then finds the disk gone and derezzes Jarvis for letting them escape before he and his henchmen give chase in their own Light Jets.

Sam is sent to the turret of the jet and manages to blast everyone except Rinzler and Clu out of the sky. As he is ordered to fire at Sam, Rinzler begins to regain his memories of being Tron and turns against Clu with the battle cry "I Fight for the Users!" As the pair battle in mid-air, Clu wins and flies after the heroes once again while Tron is left sinking to the bottom of the Sea of Simulation, being restored to himself in the process and regaining his white circuit coloration.

As the trio head toward the portal, Kevin asks Quorra to do something for him. Upon reaching their destination they are confronted by Clu, who insits he was simply following the directive Kevin programmed into him: to make a perfect world. Kevin rebutts, stating that he made a mistake in doing this and apologizes to Clu for realizing too late that they couldn't perfect the Grid. However, Clu attacks him and the bridge to the portal breaks off, separating the group. Clu then tries to steal Kevin's disk but is surprised to find Quorra's disk, and chases after Sam and Quorra as they activate the portal. Just before Clu reaches them, Kevin absorbs his counterpart into himself, destroying them both and engulfing the Grid in a tremendous explosion.

Back in the real world at long last, Sam keeps the master key in the form of a microchip-shaped necklace and pages Alan, telling him he was right about everything and will take control of ENCOM with Alan as chairman. As he leaves the arcade, he finds Quorra outside and she asks what they will do now. Sam then takes her on a ride on his motorcycle, showing her the real world.