Fandom: FMA, but sort-of AU-ish
Title: The Unweaving
Chapter: 1 of probably 4
Rating: T (on Fanfiction.net); possibly lower
Summary: Alphonse Elric has finally regained his body, but now both he and Roy Mustang have to deal with life without Ed, as Mustang gradually uncovers a horrifying truth.
Chapter 1 at Fanfiction.net