X-Mansion, Logan wants his government files and thinks Nick Fury is able to get it for him. Wolverine gets Forge to tell him that the SHIELD helecarrier was docked at the top of the Citicorp building in midtown Manhattan.

New York City, mid Manhattan, Logan rides his motorcycle into the Citicorp’s building and boards an elevator. SHIELD agents wait for him at the elevator at the top of the building. Wolverine pushes his bike up the stairs, then jumps his bike of the side of the building and breaks through the windows of the bridge of the helecarrier, pulls up to Nick Fury and demands access to national security files on himself. Elsewhere, In office building, a warning flag pops up in their computer when SHEILD accessed the Logan's files. One of the men goes and tells their leader, the leader of Hydra.

Next day, Washington DC, Logan barges into the U.S. Department of Agriculture to demand to talk with the Professor. Logan knew that he was in charge of the Weapon X project. Logan smells the Professor and Hines hiding in their office. Logan tells the secretary that if he really wanted to, he could cut down the door to his office, but tells her that he is going to get the Professor legally. Logan tells Hines to stop following him and that he is going to get evidence from the warehouse in Windsor, Ontario. Behind the office door, Hines scared tells the professor that Shiva can't stop him. The Professor decides that they should go to the warehouse to see if Shiva does its job.

In the X-Men's Blackbird, Cyclops, Jean Grey, Jubilee, and Professor Xavier help Wolverine investigate his past while taking to the warehouse. Wolverine enters the warehouse alone. Inside, Wolverine sees many soundstages, some of the stages are from his memories. Logan gets upset wondering if his past is just a cheap movie. Wolverine slashes through the sets as he walks through them, he recalls memories that he believed to be true, but might be fake. Outside the Warehouse, the Professor and Hines show up and enter through a back alley door and heads to the control room, where they can observe what Wolverine was doing. The leader of Hydra shows up with her men and watch Wolverine and the Professor from afar. Logan walk down stair and falls down a trap door, he managed to stop his fall by stabbing his claws in the side of the wall. Wolverine pulls himself out and finds a huge vault door that he couldn't cut through. Wolverine opens the vault door with the extra key on car key ring from the Lotus Seven. As the door open it glows with light, a huge machine punches Wolverine back. The machine tells Wolverine that it is Shiva, the Destroyer. Wolverine quickly dismembers Shiva, but the Professor launches another Shiva loose and it battles Logan. The Professor tells Hines that Shiva is a program that learns from its mistakes.

On blackbird, Professor X and Jubilee broke into the Weapon X program files, learning that the purpose of the project was to create super-soldiers by mind-wiping their memories, release them back into the public, re-activate them when you need them. Jubilee finds a list of seven names, Wolverine, Sabretooth, Silver Fox, Kestrel, Vole, Mastodon and Wildcat. Professor X discovers its termination list for the Weapon X project.

In the warehouse, Logan and Shiva continue to battle. In the control room, The leader of the Hydra knocks out Hines, and threatens the professor. The professor ask how she knows him. She reviles that she is SilverFox. SilverFox is shocked at the movie sets, because she has memories of those places. Shiva activates neuro-synthetic implants in Wolverine's brain, causing a flood of suppressed trauma and memories. Wolverine overcomes his memories and destroys this Shiva. Professor X, Jean, Jubilee and Cyclops arrive in time to see Wolverine cut Shiva to pieces. SilverFox remember Logan from her senior Prom and from their cabin. The Professor tries to get the gun away from her. They make their way to the control room, they discover the Professor dead. Hines was coming to. The professor lay dead, but his hook hand had been on both the reset and default switches on the Shiva override, the new Shivas were chanting the name Sabretooth as they left the warehouse. Professor X tells them that Shiva has moved on to the next mutant in the list for termination and fears that Wolverine has forever been changed by finding out some of his memories are false.