I'm looking for two specific stories to do with SHIELD. I'm not sure about pairings in either story.
1) Steve decides he needs something to do and becomes an actual Agent of SHIELD. He gets sent on missions with Clint and/or Natasha and may or may not work as their handler since they don't really trust anyone else to do the job after Coulson's death.
2) Probably pre-Avengers, Clint is used by Fury to flush out incompetent handlers.
- ETA: found