It's a Buffy/X-Men crossover, with a Spike/Xander/Wolverine pairing.
Xander, for one reason or another, leaves Sunnydale. He meets Logan (Wolverine) and travels with him. The longer they are together the more feral Xander gets. He's a mutant and he absorbs mutations around him. After they come across a mutant being attacked and then rescue him, they head to Xavier's to get the mutant (Jason?) help. Spike has been tracking Xander and eventually catches up to him at Xavier's. Xander heals Warren's wings (they go from metal to flesh). Xander gets kidnapped. Logan and Spike go after him and get him back. Somehow the three hook up together -- Logan and Spike decide to share Xander, and each other.
Ring any bells?
Edit: It's been found! The Dopplegang Effect by Becka. Thank you darkhavens!