Post apocalyptic, soldier!dean, scientist! Sam
The fic I'm looking for I read a couple years ago. I'm tempted to say it was like a book--a lot of chapters and details. Sam and Dean were living in The Bunker after the war with Angel's ended. There was a virus that killed infants very quickly and Sam was working on a cure at some outpost/rural city that begged them for help to survive. People are demoralized. Dean denied his feelings for Sam and hooked up with human Castiel because he was worried about the incest being found out. Dean is like a commander or general. There's a bar that everyone hangs out at and finds partners at. Dean goes into the city and gets Sam a kitten at one point. Sam and Dean follow Castiel after Dean ends it with him and he's in an old church going through a ritual attempting to get his grace back or into heaven or absolution for getting between Sam and Dean. There's a Doctor working with Sam that encourages his relationship with Dean.