I can't quite remember how the story gets started, but for some reason Sam calls John when he notices demons while at Stanford before Jess dies and Sam and John hunt for the yellow-eyed demon while Dean hunts (possibly with Cas?) by himself as he tries to find John and clean up behind Sam and John.

There is a scene with Dean and Michael where both Sam and John seem to reject him (I think Sam says that he wants to hunt because he's making a difference) and Michael says that isn't Dean tired of coming in second and never being enough for John. And Dean recognizes that his family doesn't value him beyond what he can do for them but he still doesn't say yes, because his job is to protect Sam and protect the family and even if he knows Sam and John don't value him that's what he does.

Any help to find it would be very much appreciated! I think it might be on AO3.