Okay, so, this is a fic where Dean (and Sam?) were abducted very young. John has been looking for them ever since, while I'm pretty sure Mary is still alive but has given up the search and gone back into hunting. John is in contact with Bobby, doing odd jobs for him. Not hunting, I don't think.
He's running an errand in some city when he somehow runs into Sam or Dean, but loses them. I think. Something to do with him showing people a photo. When he finally finds them again, it's in some kind of abandoned warehouse where they're playing.
When Dean spots him he kicks him and calls him a perv and tries to escape on their bike. I think they split up? One of them gets hit by a car, and John takes him to the hospital.
That's all I can remember. I was pretty sure it was on fanfiction.net but the search is not helping much.