History

John Wraith

Logan worked under the Weapon X program, headed by Col. John Wraith. Weapon X is SHIELD's premier counter-terrorism division. In these days, Wraith used to repeatedly shoot Logan for amusement and then watch the healing factor kick in. Wraith knew that Logan’s mind was wiped. (Ultimate X-Men #2, 7)

Two years ago, Wolverine escaped from Weapon X's Canadian facility. Since then, Weapon X has had 3 reallocations in as many months, and 6 different addresses. (Ultimate X-Men #7)
Years later, Nightcrawler will himself attempt to escape Weapon X. No mutant aside from Wolverine has ever made it as far away from the complex as he does. (Ultimate X-Men #7)

In the Savage Land, Magneto is watching video tape of the X-Men and realizes that Xavier is still alive. Magneto then decides that it’s time to send another mutant to take care of Xavier - Logan (Ultimate X-Men #1).
However, Magneto had told the Weapon X project to expect him - part of his plan so that Wolverine could infiltrate the X-Men without suspicion. Logan was unaware of this plan, and thus is re-captured.
Xavier calls his team into the school viewing room. Cerebro has located another mutant in the New York Area: Logan. Scott and Jean are surprised that they’d try to save the deadliest man in the shadow world of government black ops, but they go along with the plan. John Wraith
In Syracuse, New York, Logan is being held in a security sixteen wheeler. As he wakes up, Col. John Wraith welcomes him back to Weapon X. Since the bars of his cell are made of Adamantium, Logan is unable to escape. Wraith intends to wipe Logan’s mind again and bring him back to Weapon X.
When Beast hacked into the system to free him, Logan grabs a motorcycle and sets out after Wraith, who is speeding away in a jeep. The X-Men chase behind but are too late. The driver is dead, and Logan is waiting to kill Wraith, but the Jean is quick to stop Logan from killing the man with her telekinesis. The X-Men grab Logan and escape. (Ultimate X-Men #2)

Beast puts Logan through a highly sophisticated virtual reality system in which he slaughters the X-Men. Xavier congratulates Logan on his performance, at least in a primal sense, then asks why he's still with them, given his loner nature. Logan looks at Jean and responds "the scenery." However, the X-Men are called away: the Brotherhood has captured the President's daughter and will kill her if the Sentinels are not recalled. Wolverine opts to join the mission.
In Crotia, Wolverine does indeed help the X-Men incapacitate the Brotherhood and locate the President's daughter, but Colossus sees that Magneto has arrived (Ultimate X-Men #3).

After the X-Men escape, Scarlet Witch wonders why Wolverine hasn’t killed Xavier yet. Magneto chastises her for her stupidity - Wolverine has always succeeded and there’s only one reason why he hasn’t killed him yet - he’s trying to seduce a woman. Logan/Jean/Cyclops
Back at the Xavier Institute, Wolverine asks her how she feels about him. She doesn’t like him, she doesn’t trust him, and even though she can’t read his thoughts, she knows that he’s here for the wrong reasons. She wishes that they never met. He asks why, then, does she find him attractive. Then they kiss, passionately. And under Cyclops’ watchful eye. Wolverine is aware of this and seems to know that he’s causing problems.
This is the final straw for Cyclops, and he leaves the X-Men. In the Savage Land, he is welcomed by Magneto (Ultimate X-Men #4).
In Washington DC, Jean and Logan are watching TV footage of the British explosions inside an opulent hotel. Jean’s trying to raise Cyclops on the comm-link but he’s not answering. She feels that his leaving had something to do with her. Yet she gets back into bed with Logan (Ultimate X-Men #5).

Meanwhile, Logan revealed to Jean the real reason he joined the team: to kill Professor X while working for Magneto. But he’s started to believe in Xavier’s dream, and has turned to the side of good.
When Bolivar Trask’s Sentinels reach Washington DC - reprogramed by Magneto to attack non-mutants, the X-Men atempt to stop them. Against Jean’s wishes, Wolverine is speeding into the conflict as well. He’s convinced that Xavier can’t handle Magneto and he’s heading there to even the odds.
Magneto is about to kill Xavier, but Wolverine disembowels him. Magneto’s in shock. Wolverine tells him that he’s playing for the other team, that he likes the new option he’s been presented with - the ability to teach everyone that even mutants are human. Nonetheless, Magneto uses his powers to drive a metal pole directly into Wolverine’s spine. Quicksilver arrives and removes Magneto's helmet, leaving him prone to Xavier's mental powers, and uses Magneto's own power against him. Magneto apparently dies.
Back at the Institute, Cyclops and Xavier discuss Logan. Xavier says that he’s more than welcome but he’s leaving to take care of some personal business. (Ultimate X-Men #6)

At Weapon X headquarters in Finland, Kurt Wagner of Weapon X is trying to escape. He is marked with 'X3' on his arm. Just a few months prior, Dr Cornelius had discovered him.
Soldiers are deployed, but are ordered by Cornelius to bring him back alive. Col. Wraith manages to take him down. No mutant aside from Wolverine has ever made it that far away from the complex.
Logan, meanwhile, inspects an abandoned Weapon X headquarters in Arizona. It's been abandoned for 6 weeks. Though Xavier believes it is beause the President is keeping his word to close down all state-funded schemes where mutants were outinely abused, Logan believes it is something else. Perhaps they are afraid of him.
At the institute, Jean’s still resentful of logan's motives for joining the group. She wants him out of the group as soon as possible.
In Toyko, where Storm, Cyclops and Colossus are making a television appearance, they are immediately swarmed with fans. From out of the crowd, a woman (Rogue) removes her glove and casually brushes her hand against Colossus. Back in the Blackbird, Storm notices that Colossus looks a little tired.
Rogue reports bck to Wraith in Finland. Rogue’s done her job well - she’s got all the information and is ready to head back. She wonders is this means that they’re still gonna break all her arms and legs again. Wraith doesn’t promise her anything, but orders Divisions Beta, Gamma, and Delta from the Savage Lands who were looking for Magneto's Brotherhood initiates and send them to the X-Mansion. (Ultimate X-Men #7)

As the X-Men investigate Logan`s past, the team is confronted by another member of the Weapon X Program! And watching from the shadows are two even more dangerous operatives! (Ultimate X-Men #8)

While Professor X and his X-Men are "re-educated" in the Weapon X facility, the nation`s most dangerous spy is asked to lead a group of Weapon X mutants on a top secret, Third World mission. His name is Nick Fury - and he`s none too comfortable with how the government is treating his super-powered colleagues! But with the interests of the Free World at stake, does he have a choice? (Ultimate X-Men #9)

The team faces deadly decisions in "Return to Weapon X" part 4 of 6. The X-Men are in the hands of the Weapon X program - and John Wraith intends to make them over in the program's own dark image, beginning with a mission that will force Marvel Girl to make a unspeakable choice. Meanwhile, Wolverine desperately tracks his teammates-and enlists the aid of the recently resigned Nick Fury. (Ultimate X-Men #10) Sabretooth

The X-Men have been fully integrated into the Weapon X Program - and are at the center of a conspiracy that could plunge the planet into World War III! What is Colonel John Wraith's insane plan - and why is Professor Charles Xavier the key to it? Meanwhile, the only X-Man who remains free - the wild card known as Wolverine - finds an ally in the soldier known as Nick Fury! (Ultimate X-Men #11)

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