Recovery took weeks for the bed sores and months for the muscle wasting. His internal bits recovered the fastest; he would have had them removed entirely, but no one would agree to do the surgery in one of his labs and he refused to set foot on the medical floor or allow himself to be vulnerable in a hospital.
His mind... well, to say he wasn't coping well with this latest kidnapping would be putting it mildly.
He began researching the neuroscience of traumatic memories while still bed-bound after his rescue. Rhodey convinced him to talk to a shrink, which lasted a total of two visits before he summarily declared he was going to fix things himself.
As soon as he was able to move freely and tend to his own needs, he dismissed the home health nurse and holed up on one of his research and development floors to work out the kernel of an idea he'd developed as a result of his research. Rhodey was more persistent than the nurse and insisted that he continue to allow the physical therapist to visit, which he did.
Eventually Rhodey needed to leave to return to the Avengers but made Tony promise to send regular messages so he could be sure all was well. Tony promptly automated the updates, directing Friday to send them once daily as long as she was running and he was breathing. Any attempt to take her offline would be met with a distress signal broadcast to both Rhodey and Pepper. It wasn't much, but it would do.
His lawyer lady came to visit semi regularly to keep him updated on the trials of those arrested at the tower and the case being developed against Fury and Hill, should they be located. A manhunt remained underway, but he knew they were smart enough to evade traditional law enforcement officers. He double- and triple-checked his security measures and tried not to think about them.
The invitation to speak at MIT came just as he was admiring the prototype for his retroframing system and he said yes without thinking too hard about it. He'd owed them a talk for years, and he needed to do it to prove to himself that he could, that he was more than what the Avengers had made of him.
Being confronted by the woman from the State Department was unexpected but not surprising once he found out Ross's endgame in sending her. Secretary Ross was a slimy bastard like Fury and Hill and Tony didn't trust him as far as he could throw him, but the Accords seemed promising on a number of fronts.
Ross thought he agreed out of guilt. But while there was guilt in spades, over the civilians in Sokovia especially, that was only a small part of his rationale.
No, oversight by the U.N. meant abuse like what he'd suffered was that much less likely to happen, and that made all the difference.
He looked at Wanda, at that kid in Queens who he still needed to talk to, at the other emerging superpeople, and knew he couldn't allow his experience to become theirs.
Most of all, he couldn't allow his children to suffer such indignities.
Natasha had given him the names and details of his children as soon as she thought him ready for the information. He could not bring himself to look at it for weeks, but even so, the mere idea of a Fury or a Hill using one of them the way he'd been used had him wishing he could Hulk out and destroy anyone and anything that threatened them.
He set up trust funds for each of them. His lawyer offered to sue for guardianship, but he wasn't ready for that. He was still deeply ambivalent about the idea of kids, much less the fact that he had three.
When he'd finally looked at the files Natasha provided-on paper, because digital could end up on the internet-he was relieved that all three were at that mutant school. He'd heard good things about the place, and he was reasonably certain they were as safe there as they could be anywhere.
Almost as soon as he'd learned that tidbit, a note arrived from Professor X himself, the freaky bastard, inviting Tony to visit and meet with him whether he chose to see the children or not. He kept the offer in reserve for when the MIT thing was done.
After Siberia happened, the trials of his abusers at the tower threatened to be undone by his steadfast refusal to allow the lawyers to reveal his identity. Faced with the possibility of every single individual getting off scot-free when he still had nightmares, he decided to go public.
It wasn't an easy decision and was made in consultation with his therapist-and yes, he had a therapist now because at this point there was no way he could live without one. The trials concluded with convictions in every single case and he took it one step further.
After he had his lawyer file the custody paperwork, Tony contacted Christine Everhart and gave her the exclusive tell-all interview of her life.
As soon as the interview aired, it seemed like the world exploded. There was a frenzy of speculation about whether SHIELD had other such 'contracts' and if the disappearances of various individuals over the years were related. Calls for the dissolution of the Avengers organization were strident and coming from all sides. Doubts about whether so-called superheroes could be trusted were widespread, especially with this coming so closely on the heels of the debacle that was Budapest and Leipzig. Warrants were issued for those with a role in his abuse, especially Fury and Hill.
Tony let his lawyers and the press people handle things while he took a solitary drive to the mutant school. Rhodey offered to accompany him, but he needed to do this alone.
He strolled slowly up to the stately building, hearing the shouts of playing children from somewhere out of sight, and wondered if he was doing the right thing. For a moment he thought about turning back, but straightened his shoulders and plowed ahead.
The front door opened as he approached, a bald man in a wheelchair coming into view. "Tony," he said warmly. "Welcome."
A/N: In retrospect, aspects of this ending don't quite make logical sense, but I'd rather acknowledge it and move on than try to fix it when my brain is already well beyond this and into post-Infinity War land. :-)