This one is super vague, but I read a story where, shortly after the Avengers Battle of Manhattan, SHIELD undergoes sudden changes in management.
Nick Fury had been ousted and replaced with a Nicole Fury.
Clint Barton had been held by SHIELD for 'debriefing' following the events of the film but, as soon as SHIELD recovered the scepter, was used as a test subject for exploring the limits and control over the scepter.
Tony Stark visited the SHIELD carrier and briefly met with Nicole Fury. A mid-tier scientist/agent was able to slip him some information in a micro-storage device encased in a magnet and surreptitiously attached to the Iron Man suit, and then the agent was killed shortly after (maybe by a mind-controlled Clint?).
I would love to read this one again -- I think Clint's trauma-and-recovery plot had been handled really well. Does it sound familiar to anyone?