Born the son of Kevin Flynn, Sam was left bereft of both parents after his father disappeared some time after the death of his mother. Though watched over in his youth by his grandparents and his father's old business partner Alan Bradley, Sam developed a rebellious nature. He was later tricked into entering the virtual world of the Grid by Clu, his father's virtual clone, who sought to use Sam to get to his father. After being captured and forced into combat against Clu's enforcer Rinzler and then Clu himself, he was rescued by Quorra, a program and student of his father's.
After reuniting with his father, Sam became frustrated with Kevin's approach of waiting for things to develop and set out to find a way to return to the human world on his own. This ended up alerting Clu to Kevin's location, spurring on events towards a final confrontation. Along the way, Sam learned that Quorra was the last of the ISOs, a race of beings who had developed spontaneously within the Grid. The two bond, and later escape into the real world using Kevin's identity disk while Kevin sacrifices himself to destroy Clu and save both worlds.