The story starts with Steve waking up from his frozen state, and SHIELD instead of setting him free, keeps him as a prisoner. Eventually he is joined by Peter.
Basically, SHIELD believes that those with powers are dangerous and need to be under lock and key.
Tony is also in prison, and he stays in SHIELDs custody because they injected Pepper with a poison of some kind. He is kept prisoner with Bruce.
I believe Thor and Loki were also kept prisoners.
Towards the end, Natasha and Clint with Maria and Phil's help free the Avengers.
I think Pepper sends them to a cottage to recover, until eventually the whole team saves the world.
I am unfortunately providing a very bad summary to a very good story. It is killing me the fact I forgot to bookmark it.
Fic Found Coulson's Eleven by Copperbadge