As a kid, Sam loved to listen to Flynn's stories about Tron and the Grid, even collecting the merchandise based on them. After Flynn's disappearance, He was raised by his grandparents as his mother had already passed beforehand. By age 27, Sam had lost his grandparents and lived in a shabby apartment below the bridge with his dog, Marv. He also grew to be a thrill-seeker as he performed dangerous stunts during his annual pranks on ENCOM. He did so because he lacked interest in the company otherwise. However, he had hardened to the thought of his father returning; believing him to be dead or living peacefully on a tropical island.
However, his father's best friend and work associate, Alan Bradley, informed him that he received a page from Flynn's arcade, which had not been closed for 20 years. Sam investigated and found Flynn's lab. However, he accidentally zapped himself into the Grid, where he was mistaken for a damaged program and forced into the Games. However, his opponent, Rinzler, noticed he bled and recognized him as a User. Sam was then brought before CLU (who at first put on the charade of being Flynn due to their resemblance), who thought he would have the information on his Identity Disk to free him from the Grid. However, this proved not to go in CLU's favor and Sam was forced onto the Light Cycle arena. Sam was nearly killed by CLU, but was rescued by a program named Quorra.
Escaping with Quorra, Sam reunited with his father, who enlightened him as to why he had been trapped in the Grid for 20 years. Deciding to return home rather than listen to his father and stay to keep CLU from getting what he wants, Sam went to Tron City to met one of Quorra's old acquaintances, Zuse. However, Zuse proved to be a backstabber and turned Sam over to CLU's guards. Luckily, Quorra and Flynn arrived and rescued him, but lost Flynn's disk to Zuse. Sam, then boarded a transport heading to the exit portal. On board, he learned Quorra was the last ISO and that she was needed on the outside. When the transport arrived at CLU's re-purposing area, Sam took back Flynn's disk and they stole a flying vehicle to escape. Reaching the portal, Sam was forced by his father to leave with Quorra while CLU was destroyed. Back in the real world, Sam downloaded the Grid onto a chip and keeps it. Deciding to take responsibility of ENCOM, he names Alan Chairman of the Board and takes Quorra to see her first sunrise. Throughout the movie, Sam is shown to have a growing attraction to Quorra.
Ever since Kevin disappeared, Sam has been deeply affected by both the loss of his mother and father. He is also the heir to the largest software company in the world, which makes him feel that he can't follow in his father's footsteps. He is somewhat rebellious, reclusive, and lives modestly with his pet dog, Marv, in a shipping container reconstituted into a home on the river with a beautiful view of the city and the ENCOM Tower itself. He has a pronounced technical aptitude inherited from his father, and has applied this towards fixing Kevin's motorcycle.
- Sam Flynn is the seventh (and so far last) offspring of a predecessor's protagonist to take over in the lead role, the first being Nikki Ferris (taking over for Sharon McKendrick) in "The Parent Trap II", the second being Kiara (taking over for Simba) in "The Lion King II: Simba's Pride", the third being Melody (taking over for Ariel) in "The Little Mermaid II: Return to the Sea", the fourth being Scamp (taking over for the predecessor's title characters) in "Lady and the Tramp II: Scamp's Adventure", the fifth being Jane (taking over for Wendy) in "Return to Neverland" and the sixth being Patch (taking over for Pongo and Perdita) in "101 Dalmatians II: Patch's London Adventure".