I read a fic a while back where the avengers get a hold of sensitive Shield data and realize that there's a prisoner being held captive and tortured by Shield. They realize it's Loki, jailbreak him out, hide him in the Tower. Meanwhile, it turns out to be part of a plot by some original character (I wish I could remember this name) who's trying to get them to "impeach" Fury so he can become the new Director.
Loki's magic is bound, and he originally starts out wearing a metal collar. Towards the end of the fic, he manages to get it unbound by making Thor command him to be able to use his magic.
I think this was on A03 but I'm not sure, and I can't find any trace of this story. It was very long, complete, and probably loki/tony pairing? if any? I forget.