FYaON - Scully splits after Kitsunegari, moves to California and has no contact with Mulder for like a year-ish. He shows up one night and sleeps with her, disappears again, and then shows back up to jet off with her to Singapore because ... spoilers. As Wen implies, hot, angry sex plus adventures ensue.

babyfic - someone else mentioned it, but I like Anjou's Ghosts trilogy. I don't know if it counts because it's William, but to me, it gets pretty close to a realistic babyfic scenario. It's not picket fences and happily ever after, but it has some hope. Which I like.