Dollhouse or Dollhouse type AU. When you want the right person for the job sometimes the easiest thing to do is to create the right person. Or team of people. Luckily SHIELD/the World Security Council has enough money to make that happen (by purchasing from a Dollhouse or researching and designing this tech themselves).

In which the Avengers (formed by SHIELD)/SHIELD (formed by the World Security Council) are a team of people brought together to deal with threats...but they aren't necessarily who they think they are. Natasha has had experience of this kind of thing before, Clint has been affected by the Tesseract/cognitive recalibration/falling off another damn building, and the pair of them start decontructing the roles they find themselves in and their identities.