Adversaries by Hilary. This is one I found through one of my all time favorite fic rec lists -
seanachais. Sort of, at least; it required some leet internet search engine skillzz on my part because the link on her site was dead. It was well worth the search, though, because it really is a great Long And Plotty story. It involves another Prophecy, but don't let that stop you because it is amazingly well done. Can't really say more without giving away some of the key twists, but still - for Buffy the Vampire Slayer fans (and even those of you who are Fans By Association, like me), this is well worth a read. I ScrapBooked it as soon as I finished reading it.