I think that's what we're unsure about though, right? Would destroying Clu in any fashion have destroyed Flynn too? They weren't all that clear about that in the film, as I recall, though I can't remember Flynn's and Quorra's exact words on the subject.

Destroying Clu would not have done anything to Flynn, I think. They were not linked, Flynn returned to the real world without harm many times. Flynn probably rebooted that computer and did lots of editing on the keyboard in the real world without any adverse effects to his real/digital versions.

I think of the reintegration akin to what would happen if you had donated a lung to someone, and then suddenly had that lung put back into to you. The other person dies and a very good chance your body would reject it even though it originally came from you.

So the question is, why didn't Flynn just destroy Clu directly. I think he tried, but Clu would actively thwart his moves. Kind of like trying to catch a flea, Clu would use everything in his power never to get in a position of head to head combat on equal terms. I don't think Clu could kill Flynn, but imprisonment is just as bad. So they both were exceedingly good at staying out of each others grasps.

The end confrontation, Clu still doesn't kill Flynn even when he has every reason to and Flynn would have let him, but Flynn knows as Clu demonstrated that he wouldn't do it (at least he was 'pretty' sure, there is some hesitation there). Still, a kick to the face is far from gentle.

MCComputer - Good question regarding whether or not a user can be derezzed. I have often wondered that myself. So far, no users have "died" in the grid in this series...not counting Flynn's explosion / implosion. Would they derezz or just bleed to death or what?!? The only injury is Sam and he bled so I guess if a user was killed, all of the programs would just stand around wondering what all that stuff inside of him is. Like humans dissecting an alien. Would his body just disappear or would the programs on the grid have to deal w/ disposal? Would they autopsy the body or just create a shrine...would the body decompose?

I'm assuming any users would just fade out after they die since the data they are composed of simply ceases to be.