Weapon X facility, Logan wakes up strapped to a table with the Weapon X helmet one. The director sits in the shadows and welcomes Logan, they remove the helmet since it was outdated technology. Logan ask what’s going and where is Sabretooth. The Director tells Logan that they are healing his wounds, Sabretooth is on another mission and that the Weapon X project has been re instated under his control. the director ask if Logan remembers him, but Logan doesn’t, so the Director tells him his story.

In the Past, the Director was assigned to be a guard in a US/Canadian operation at the original Weapon X facility. The Director says he was young and naive and jump at the opportunity, only being on the job for a few days he says Logan escaped. Logan cut and slashes everyone and everything in sight, nothing could stop Logan. That’s when Logan saw the Director and came over and slashed at his body, then carved into his face, tearing his limps off, the Logan let out a howl and ran off into the forest. Soldiers soon found the Director in pieces and after much operations and procedures his body was restored, but his face would never look the same again, not even plastic surgery could restore it, so he left it as a reminder of what happened. The Director continued to work for the government, but they hid him away in a office, so that no one would have to see him. the director became obsessed with reinstating the Weapon X project and finally after Senator Kelly got assassinated Project X was approved and that when they went back to the original Weapon X facility and found the program that originally controlled Logan, they began to use it to assassinate the original men involved in the project. Everything went fine until they made Logan kill Senator Walsh, then they lost control of Logan. That’s when they sent their spy Brent Jackson to lead a SHIELD mission to recover Logan. Brent Jackson sent Logan to the Cage until the could assemble a team and the codes to break Logan out.

Present, New York City Millennium hotel, Maverick meets John Wraith at room 1209. Wraith tells maverick that the Weapon X project has reformed and wants to establish the old team, Sabretooth come out and tells Maverick that the Team will be in charge of assassinating any mutant that stands in the why. Maverick grabs Wraith as a hostage and tells them that they are traitors to mutant kind. Maverick shots Wraith in the back and Sabretooth in the leg. Sabretooth pushes maverick through a wall and then throws him through a window. Sabretooth looks out the window to make sure maverick fell to his death, but their wasn't anybody. Maverick drops a bomb, which blows Sabretooth out the window. Sabretooth gets back up the roof, Maverick opens fire, Sabretooth throws maverick to the floor. maverick uses his mutant power and blast Sabretooth back, Maverick goes to kill Sabretooth, but Sabretooth stabs his whole fist into Maverick’s chest. Sabretooth tells Maverick that he can change his mind and join the team. Maverick spits in his face and Sabretooth throws him off the roof. maverick falls 20 floors and slams to the ground.

Weapon X facility, two guards talk about how the Director's disfigured face makes them want to puke, the continue to patrol level 6, when suddenly Shiver Man appears out of thin air and kills them both.

Elsewhere in the facility, the Director offers Logan his real memories back, to clear his record of the murder, if he will join Weapon X project and help them ride the world of any mutant that won't join the cause. Logan tells the Director that sounds tempting, but he rather break free and carve his face up even more and threaten to kill Brent Jackson. The Director tells his doctors, Dr. Duncan and Dr. Zira to prepare Logan for memory re-implantation. Shiver Man appears and shots up the implantation machine. The Director and Brent Jackson hide, while Shiver Man phases Logan free from machine. Shiver Man tell Logan that he knows that Logan is innocent and they are not. Logan sees the Director and Brent and leaps at them, but they teleport away just in time. Weapon X guards block the exit, Logan tell Shiver Man to please find Beast for him, while he takes car of the guards.

New York City Millennium hotel, Sabretooth goes back to the room, Wraith lays on the floor bleeding and ask for Sabretooth to call the program so they can fix him. Sabretooth tells Wraith even though he works for the Weapon X program he still has his own agenda and doesn’t want Wraith around to tell on him, since he is loyal to the project. Sabretooth breaks Wraiths neck, then gets a call that they are going to teleport him back at base as a reinforcement.

Weapon X facility, Logan tears through the patrol of guards and tells the Director of the radio that hes coming for him. The Director order that all remaining staff to teleport to the nearest Weapon X base and to start this bases self destruct program. Logan heads for the exit, when Sabretooth appears and slashes Logan in the neck, Logan kick Sabretooth in the neck, picks him up with his claws and slam him to the ground. Sabretooth kicks Logan off, slashes him in the face, picks Logan up and slams him knee. Shiver Man appears and shots Sabretooth in the back, Logan grabs Beast and run out of the facility, just as it explodes. Shiver Man appears out of the debris, Logan ask what happen to Sabretooth, but Shiver Man just keeps walking.

Several days later, Logan sits at a table with Nick Fury, Nick Fury explains that he has covered up Logan's involvement in the murder of Senator Walsh, so that all mutants don't have to suffer for it, but in doing so also had to cover up Weapon X projects involvement too.

Elsewhere, Brent Jackson ask the Director if Logan's new implants took, but the Director tells him that only time will tell, but Logan was just the beginning of what they have planned.