The agent who had captured Clint became his handler. I recall Clint either having a choice/being asked if the arrangement was okay with him, and of course he said yes, because this agent was the only person who knew about the mind control, and was therefore the only handler who wouldn't give him orders he couldn't escape.
The agent eventually died in a car crash, and Coulson became Clint's new handler. Clint didn't like him at first, but slowly grew to trust him. I don't think that Coulson gave out orders much, but other agents did. I recall a scene where a fellow agent (Sitwell?) had told Clint to go jump off the helicarrier as a joke, and Clint, having no other choice, jumped, but was saved at the last minute.
The rest of the fic deals with the events of the Avengers and how working in a team dynamic affected Clint. The rest of the team eventually found out after a mission in the jungle went wrong -- Coulson hadn't been there, and Clint's current handler had ordered him to put himself into a dangerous situation. The rest of the Avengers watched the incident go down via video feed and realized that that Clint wasn't himself. The rest of the story slowly came out.
I don't remember much else, just that Fury fired Clint and that broke the mind control for some reason.
It was up on ff.net, as I recall, and was Clint/Coulson preslash. If anyone could help me, that'd be great -- I've been looking for this fic forever!