Pairing: So far Rinzler/Clu, and the author has mentioned possible Clu/Jarvis/Rinzler in the future.
Synopsis: Clu's plan succeeds, and he manages to bring his army into the real world, where he gets a nasty shock. None of the fighting methods his soldiers know are especially useful in the user world. Throwing a disk does nothing except maybe annoy the person it bounces off of, he can't manipulate the environment in any way, and guns? What's a gun?
Comments: The only Tron fic I've ever read that makes me cheer on Clu. This has a rather heavy dose of Humans Are Bastards, but if that doesn't bother you, this is possibly one of the best fics on the meme. Right up there with We Are Pilots. It's ongoing, but the author updates very quickly, considering the length, detail, and lack of mistakes.
AFAIK, we can't link directly to kink memes since the Content Policy change, so I pulled this:
Rectify
by Aldhibah (Link is to the Kink Meme thread.)