I've read several Magnificent Seven stories with this story theme and one Avengers story with one close enough to be considered in the same vein. (Where Coulson wakes up weeks after the Battle of NY in a hospital some distance from SHIELD and the Tower, surprised that there no sign of any visitors. Turns out that he'd been taken to a hospital in another state and a paperwork glitch made everyone think he was dead.) Like Ezra Standish in Magnificent Seven fic, Tony often feels the outsider, not really part of the team, the odd man out, if you will. I just read a story where the only way to get Tony out of his lab and into bed 3 days after a battle is to almost force him into a cuddle party, with every team member touchong him in some way. Recalling M7 stories where this backfires I wondered if there were any similar stories in the Avengers. Scenes like where Standish awakes in a hospital bed with none of his teammates around, not realizing that they are actually on their way to his room but hospital elevators are notoriously slow.
Thinking about it, even a "so-and-so gets kidnapped and nobody noticed" story would work. (But kid!Tony get kidnapped and Howard never notices is not what I'm looking for.)