The one story that immediately comes to mind which specifically incorporates and revolves around the events of the episode
Enemies is
Nemesis by HollyDB. This story is actually the second installment in Holly's three-part Yellow Brick Road series, which begins with a rewrite of the episode
Helpless and runs through the remainder of Season Three. You can read the fics separately, but I'd strongly suggest reading the entire series in order. It is a very good read. All fics can be found on this site and Elysian Fields. Here are some links:
CupiditySummary: Book I of the Yellow Brick Road series. An alternate version of Season 3's Helpless, in which the Council locks a drugged and powerless Buffy in with a certain bleached-blond vampire who already has two Slayers under his belt.
NemesisSummary: Book II of the Yellow Brick Road series. While trying to cope with mixed feelings and brewing hostility, the Slayer discovers the truth behind Faith's deception and attempts to deal with her suspicion about the other Slayer's seemingly close relationship with Angel. Conspiracies arise and explanations unfold, and when things just can't get any more confusing, a blonde vampire she was sure she would never see again decides that it's time.
L'AmourSummary: Graduation Day nears. Spike learns that some things are not better left unsaid while Buffy comes to the realization that knowing what one has is imperative before it becomes gone.
If I think of any others, I'll let you know!