The synopsis below may give away important plot points. Sam wants to go back but Flynn doesn't want to give CLU the chance to carry out his plan, so he chooses not to but Sam defies him. That's where he tells Sam that CLU turned on him and was planning to enter their world to 'fix' it's imperfections, so to stop him he closed the portal trapping himself there which is why he never came back.

Sam is saved by a program named Quorra who takes him to his father. He is brought to the head man whom Sam thinks is his father but later discovers that it's CLU and he makes Sam take part in a light cycle battle. After being mistaken for a program, he finds himself subjected to all sorts of contests but when they discover he is not a program but a user. Sam goes there and finds his father's work station and after entering a few codes finds himself in the Grid. Alan still clings to the hope that Flynn is out there and that he didn't walk away from his work and Sam, he gives Sam the keys to the arcade. Sam wonders why is that so important, Alan tells him because the number's been disconnected for 20 years. One day, Alan Bradley, his father's best friend tells Sam that he got a page from the phone at his father's office at his arcade. Sam spends his time moping over his father's disappearance and pulling a prank on the board.

20 years later, his father's company ENCOM is being operated by the Board who take the company in a different direction as oppose to Flynn's. He promises that one day he will take him to the Grid, but Flynn disappears and Sam is devastated. He talks about the friends he made and his emissary CLU which is a program he made in his likeness. In 1989, computer genius Kevin Flynn tells his young son about his adventures in the cyber world of Tron.

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