
Angelus won the fight at the end of Becoming II, but figured out how to stop Acathla. He realized, with Buffy gone, that ending the world was really kind of stupid. So he shut down Acathla, and started taking over Sunnydale.
Xander, Giles, Oz, and Cordelia carried on with the "good fight," but Willow could not. Her failure to re-ensoul Angel resulted in a mental and physical breakdown, and she is in an asylum. Xander decides to leave the gang, and get on with his life. He's just an ordinary guy, and he doesn't feel he needs to be the one fighting anymore. So he quits the Scoobs.
Angelus catches him one night, and the rest, as they say is history.
Warning: This story contains explicit scenes of torture, rape and death. It also contains bloodplay. If you are at all made uncomfortable by these things, then you really should just not read this story.