Someone (I think Doom) creates a reality where Tony died when he was really young, so when he tries to go to Shield no one knows who he is. They end up locking him up and sending him to a facility where they experiment on him and eventually give him extremis. He uses it to contact Steve and ask for help, but Steve doesn't believe him at least at first. Thought I had this one bookmarked, but I can't find it and I can't remember how it ends and it's driving me nuts!
Update: I found it! It's The World That Forgot Tony Stark
https://archiveofourown.org/works/527492/chapters/934052