I think there was a fight in a warehouse? And something was going on in the warehouse with some new weapon and it got Coulson? And then later Clint is going by Coulson's office and that's when he finds out the weapon like, scattered Coulson's consciousness and he ended up in tiny little robots? Or maybe Coulson wasn't there, but that was something that happened off screen, I'm not sure.
Mostly I only remember the nanobot part well, but I know Clint was the other main character in the fic , and it might have been pre-slash Clint/Coulson.
ETA: FOUND, thanks to bbuttercup It's softly and suddenly vanish away by Sidney Sussex.