Wolverine was the sole survivor of the massacre of the X-Men by the Director of Weapon X and his Sentinels, a direct act of revenge by Colcord against Logan. Wolverine recovered and formed his own team of X-Men out of former allies and enemies, striking back against the program. They were eventually betrayed from within, however, when Agent Zero's old post-hypnotic control words were uncovered, turning him against the team. Zero killed off most of the X-Men before regaining his senses and killing himself before he could do any more damage.
Wolverine rebuilt again, with another team of X-Men, and eventually married his old friend Carol Danvers. The mutants remained in separate factions for too long, though...while they eventually joined into a single force, the Sentinels had become too powerful. Wolverine and the others attempted a last ditch effort to use Rachel Summers and recreated her trick with Kate Pryde from the Kelly assassination years earlier, but their efforts failed to prevent their future.