I just reread the short story Best Served Cold by AvocadoLove, where Tony is left behind at the RAFT when Rogers breaks the rest of the team out. Several weeks later Tony is rescued by Barnes, without Steve's knowledge. I was reminded of a longer story which I can't seem to locate now. Hoping for some help. Tony is deliberately left behind when Rogers breaks his team out of the Raft, leaving him in the hands of Thunderbolt Ross. When Tony's new team (including Deadpool) finds out they go to rescue him. Ross has been subjecting Tony to the Chair that Hydra had used on Barnes. I think Deadpool gives up his life in the rescue mission -- that is temporary, after all.
This may be just a short story, or part of one, or part of a series. I don't recall. All I remember is the scene in the Siberian bunker. Tony shoots Steve in the face, blowing half his face off to reveal that he's a skrull, and has been for a while, maybe since Steve drove off the see the country after the Battle of New York. Ring any bells for anyone?