It's brief but, Kevin's understandable reaction upon realizing who it really is that's chasing them
Kevin: Tron, what have you become?
"I fight for the Users."
The flashback where Kevin Flynn sees the genocide of the ISO programs and realizes that there's nothing he could do to stop it.
Then we get another flashback the explains what happened to Tron.
In Fridge terms, the scene where Kevin reveals to his son that Quorra is the last ISO and all of Kevin's efforts to disguise her as a regular program. The scene when she tells Sam how she escaped the genocide only makes it worse.
Sam: Alan, you're acting like I'm going to find him sittin' at work, just, "Hey, kiddo, lost track of time."
Alan: (wistfully) Wouldn't that be something.
It's so sad to hear the formerly energetic and cool Kevin Flynn wearily say "Life has a way of moving you past wants and hopes".
Despite everything he does, Clu is a tragic character. Everything he does, it's because he was programmed to do it that way (with an astonishing lack of foresight) by a young Kevin. In the end, when Kevin confronts him, he completely breaks down because he cannot accept something he wasn't created to understand in the first place.