Continuity mistake: At the end when Flynn is asking Sam to go, Quorra has Flynn's disc on her back. In the next shot she says "Sam, it's what he wants" and the disc is no longer on her back. And then in the next shot it's on her back again before she gives it to him.
TRON: Legacy (2010)
Plot summary
Directed by: Joseph Kosinski
Starring: Jeff Bridges, Olivia Wilde, Bruce Boxleitner, Garrett Hedlund
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More mistakes in TRON: Legacy
Kevin Flynn: Your old man's about to knock on the sky and listen to the sound.
Trivia: The two 'disc jockeys' in the soundbooth of the 'End of Line' club are actually Daft Punk, the French group that created the movie's soundtrack.
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Answer: Because Clu was given all the authority of the most important user, the creator, Flynn.
Phixius ★
But what did Clu do to Tron to make him serve him? Tron fought for the Users so it would make no sense for him to suddenly side with Clu who wanted to create the perfect system and help him in annihilating the ISO's.
When Clu and co. attacked Tron and Flynn, Flynn's disc must have been damaged, removing his personality in a way similar to amnesia. This allowed Clu, now master of the system, to gain control of Tron's skills. Later, when Prinzler saw Flynn, he remembered him and what he did, and regained his original purpose.
The answer was in the movie itself. During a conversion between Sam and his father it is mentioned that Clu had the ability to repurpose programs. This is the action that allowed him to "build" the perfect system. The isos were manifested without creation from anything and had genuine freedom that Clu couldn't repurpose. This is why he destroyed them because it threatened his strategy to create perfection. Answer: Clu repurposed Tron to serve him and do his bidding. That simple.