Colonel John Wraith

Wraith was the director of the Weapon X program, a division of S.H.I.E.L.D. that would capture and incarcerate mutants to send them on dangerous missions. Wolverine was the only captive ever to escape the program, which lead Wraith to try and recapture him on many occasions. After a successful attempt to recapture Logan, the X-Men found, broke out, and recruited Wolverine, while saving Wraith's life in the process since they stopped Logan from killing him. Instead, he left him with three scars on his face from his claw marks.

Weapon X learned of the location of Xavier's institute and took everyone, except Wolverine who left a few hours earlier, captive. They did horrible things to them including turning Beast's skin blue as a side effect of increasing his strength and speed, and forcing Marvel Girl to kill a scientist so that they wouldn't detonate the neural implants inside Cyclops' head.

Wraith, and the rest of Weapon X, was finally taken down by the Brotherhood when Wolverine asked for their assistance in freeing them all. After Wraith almost escaped on a helicopter, Storm attacked him with a lightning bolt trying to kill him, but he was saved by Nightcrawler saying that he didn't want this place to turn her into a killer too. As a thank you, Wraith was about to shoot Kurt in the head when he was killed by Nick Fury, director of S.H.I.EL.D. and old friend of Wolverine, by pumping three bullets in his chest. Fury then let all the mutants free from the Weapon X program.