The story begins in 1968. Logan is walking along a backstreet, when behind him come some agents from the Weapon X program. They try to catch Logan so they can take him to the Weapon X facility. Logan tries to defend himself but he is shot with a tranquilizer dart and knocked unconscious. Logan is taken to the Facility and subjected to the adamantium bonding process. Soon after, he escapes from the experiment chamber and tries to get outside. The Professor calls him an animal in return Logan says Not animal!, showing he has still retained his humanity. Logan a.k.a. Weapon X tries to get to The Professor to confront him but he is stopped by Sabretooth. Weapon X defeats Sabretooth and he confronts The Professor while telling Dr. Abraham Cornelius and Dr. Carol Hines to leave. When Weapon X restrains him at claw-point, The Professor reveals that all Weapon X subjects were implanted with a dormant and deadly virus known as the "Sheva Strain" as a failsafe. The Professor also reveals that the virus would kill a normal human in one year but has no idea how long the virus would kill a human mutant.
Later in the present, Logan, who now goes by "Wolverine", is now a member of the X-Men and he has told Beast what he remembers of his past. Beast tells Logan/Wolverine that the Sheva Strain Virus has bypassed his healing factor and will kill him in two days if the cure is not found. Professor X tells Wolverine to try to find the cure in the Weapon X Facility while Beast provides Wolverine with a implanted wristwatch telling him how much time he has left. After being flown to Edmonton by Cyclops and Jean Grey, Wolverine uses a private plane flown by a female pilot to get to the Weapon X Facility. However, the plane is shot down. He survives the plane crash and starts making his way towards the Weapon X facility.
Wolverine fights his way to a cavern where the spirit of the Wendigo lives. Wolverine fights with Wendigo and wins. Wendigo gets up and throws Logan out of the cavern where he lands on snow. Logan sees a Weapon X truck and jumps on it. Logan reaches the Weapon X Facility and sneaks in. On the way in, he is ambushed by a group of GIs. The sound of gunfire starts and Wolverine is surprised that he's not shot. He then sees another GI who shot down the ambushers. When Wolverine asks him why he let him live by asking "Am I supposed to thank you, or are you just a lousy shot?", the GI states, "Lets just say it's not your time to die...yet." Wolverine examines him a moment and he asks "You're not quite human, are you?" To which the GI states, "You should talk." As he walks away. After fighting through the base, he access a database and finds that the Weapon X scientists are at the Void (a maximum security mutant detention center that's similar to the Vault) so he makes his way there. Leaving, he is attacked by Sabretooth again. Sabretooth is defeated and grudgingly gives Wolverine the Part B of the virus cure after stating that he knew about the Sheva Strain Virus a long time ago.
Later, Logan goes to The Void where he sees Colossus who lets him enter the facility after he was informed by Professor X about Logan's condition. While Logan is fighting his way on the Facility, Sabretooth comes to the Void and takes out some of its security on his way to get to the Weapon X scientists. Sabretooth then releases Alpha-Class mutants Omega Red, Magneto and Juggernaut from their prisons. Meanwhile, Logan finds Dr. Abraham Cornelius and Dr. Carol Hines. Abraham Cornelius gives Logan the formula of Part A of the cure. Due to the Void blocking Logan's contact with Professor X, he ends up having to head outside to relay the info to him. Upon leaving, he warns Abraham Cornelius and Carol Hines that Sabretooth is also looking for them. However, when Logan reaches the roof, he is faced by Juggernaut. When Logan defeats him, Colossus tells Wolverine that Magneto and Omega Red were the other two Alpha-Class mutants that were freed. As Colossus drags the unconscious Juggernaut back to his cell, he points to the device that will help Logan get out. Logan destroys the Void Shield and relays the info of the Part A cure to Professor X after being told that Beast has synthesized the Part B of the Sheve Strain Virus cure. Logan then heads out to find and defeat Magneto after Professor X detects magnetic signatures.
After Logan escapes, May Deuce the Mutant Hunter Boss comes to the Void to lead the Mutant Hunters into hunting down Wolverine and the other escaped mutants. While looking for Magneto, Logan is contacted by Professor X stating that the Magnetic Flux Limiter Collar on him has suppressed Magneto's magnetic powers long enough for him to become more powerful. Logan comes across a ruined highway and uses a motorcycle which he rides into a ruined town. Logan manages to find Magneto in a steel mill. Logan tries to stop Magneto's moves, but he has to kill all the Mutant Hunters at the same time. Logan defeats Magneto and knocks him unconscious. Upon being told by Professor X that too much magnetic interference is preventing Rogue from homing in on him, Logan then makes his way to the city leaving Magneto for any Mutant Hunters sent from the Void.
When Logan is heading to the city to meet up with Rogue, a helicopter comes to him. In the helicopter is May Deuce. She thanks Logan because he defeated Magneto and offers to take him to the top of the Xenon Building. But when the helicopter reaches the top of a building, May Deuce throws Wolverine on the roof. Logan sees Lady Deathstrike and he realizes that the pilot, the Army GI, and May Deuce were some of Lady Deathstrike's robots who were to direct Wolverine to her so she could kill him. She also revealed that she paid Sabretooth to cause him pain. Wolverine defeats Lady Deathstrike and reaches a helicopter land platform where she follows him. Logan throws Lady Deathstrike off the roof and Rogue comes with the virus cure. Wolverine drinks it and goes home. Sabretooth finds Lady Deathstrike. He takes a vial from her and drinks it (most likely the cure for the virus), takes her, and leaves.
Meanwhile, Apocalypse and Mister Sinister watch every move from Wolverine as they prepare their Horsemen of Apocalypse.
Wolverine lies on his bed and then suddenly realizes that he hasn't found and defeated Omega Red upon remembering the escaped mutants that Colossus told him about.
- The game is not based in the movie universe. They advertised it for a competition to get free tickets to see X2: X-Men United.
- Lady Deathstrike
- The Professor
- Dr. Cornelius
- Mr. Sinister