There didn't seem to be any pairings, not to the point that I read. It focuses on Tony Stark and is very subjective in both the timeline and what 'really' happens. It's a captivity story, though it's not a typical one in that it's not the terrorists or enemies of SHIELD who take Tony hostage. There is a suicide attempt from Tony (he begins to repeatedly hit his head against the wall), but the reader finds out later that he wasn't 'serious' about it; he purposefully injured himself to the point where his captors (who we discover are the Avengers and Fury, though he doesn't know this) are forced to take him to a medical bay for treatment.
Tony is forced to see a therapist and it's during the written sessions that the reader sees just how truly subjective things are: he thinks that he's been stuck in the suite of rooms for 3+ months, but--in actuality--it's been... 2 weeks? 3 weeks? I can't remember. But it's right about then that the reader starts to realize that Tony's reality is distorted and things aren't really what they seem.
One of the most vivid scenes that I can remember is when Tony wakes up in the med bay and he's surrounded by all the other Avengers. He's happy and relieved and says "I knew you guys would come for me" (or something to that affect). Pretty much right then, the Avengers' faces fall because they realize that Tony doesn't remember just why he was put in the suite of rooms--a villain appeared who could control minds and focused on Tony. He manage to take over Tony's mind while he was wearing his suit and he ended up hurting his teammates and, before things got really bad, he told the others "Do it" and so they put him in confinement and had been searching for the villain ever since. Anyway, Tony completely blanks on this and distances himself from the Avengers because he feels betrayed and, eventually, decides to let JARVIS show him recordings to finally see what he can't remember. That's the last that I can recall of this story.
I honestly can't remember if I read it on fanfiction.net or ao3, but I've been trying to search both sites for the story and... no luck thus far. Does anyone know what I'm talking about and/or has a link to the fic?