-Late one rainy night in a prestigious museum, the master thief Fantomex pulls off an incredible heist. Before he can make a clean get-away, however, he is confronted by a mysterious old man: Dr. Malcom Colcord. After refusing to answer questions about his past, Fantomex tries to flee but is overpowered by Omega Red. Colcord announces he has "great plans" for his newest prize.
-We find Wolverine on the Xavier estate, struggling to adjust to his new home following the events of "X-Men: Dangerous Game". He is plagued by nightmares alluding to shattered fragments of his forgotten past and a mess of insecurities and regrets about what past he can remember. No matter what they X-Men say, it's clear to himself that he doesn't belong here.
-Hisako Ichiki, otherwise known as Armor, thinks differently. She sees in him an injured warrior who she can connect with in a way that none of the teachers at the school have. Nonetheless, Logan continues to push her away. When a news story triggers something in his hazy memory, he flees into the night, not realizng that Hisako is tracking him.
-Logan returns home to Canada, but on the way must help save Hisako from a gang when she reveals herself and risks making a scene with her flashy powers. She refuses to leave, and he begrudgingly takes her along to a wilderness lodge run by Heather Hudson and John Wraith, two old friends of Logan who he can barely remember. Logan's time at Weapon X is delved into, leading up to the collpse of the program after Jim Hudson blew the whistle on increasingly immoral expiraments, an effort he paid for with his life.
-Heather explains that old Weapon X sites have been raided and files stolen, while past subjects and employees have begun to disappear, with some turning up dead. She and John have linked these attacks to a mysterious figure who seems to be aided by one Brenda Jackson: ex-SHIELD, ex-Hydra. We see the villains in action again, now forcing Fantomex to do their bidding. Colcord's past involvement with the program and Wolverine is hinted at, as his facial scars are revealed.
-A deal has been set up as a trap for the mystery man. Logan, Wraith, and Armor go to stop it. Before he leaves, Heather lets Logan know that she sees something new in him, and that maybe it's time to stop running. At the drop-off point, everything goes south. Fantomex takes on the heroes and beats them before fleeing. He catches the tracer that Armor placed on him, but leaves it there nonetheless.
-The chase leads overseas to Russia, where Colcord has set up base in the abandoned KGB Weapon X branch. He is frustrated that so few of his expiraments are working. Jackson suggests the start using the fit subjects to study, but Colcord insists he needs them if he can hope to capture Wolverine, his end goal and the ultimate creation of the program.
-In Russia, our heroes fight their way through gathering leads on Colcord's operation. Armor reveals that she brought along a costume that was designed for Logan, however he refuses to wear it. But they raise a bit too much attention. An ambush is triggered by Omega Red and Fantomex. Omega Red kills Wraith and Armor and Logan are taken prisoner.
-They are taken back to the base. Logan offers himself up for experimentation if Hisako is spared. He is taken into a lab, and Fantomex is ordered to imprison Hisako. Instead, he turns on his masters and sets the lab into meltdown, releasing all the subjects and causing mass chaos. Colcord, meanwhile, has revealed his origin: A mere guard for the original Weapon X, he was scarred when Wolverine went rougue, and blames him for the collapse of a program he believed was viatl to ushering in a new era of "peace through strength".
-When all hell breaks loose, Jackson abandons Colcord and flees with his data. The Doctor cuts his losses and tries to flee with Logan on a plane. Armor and Fantomex pursue and the ensuing fight crashes the plane. WIth his friends down for the count. Wolverine stands alone. Colcord mocks him for being always alone, with no family or friends to turn to. The only thing Logan has left is to give up his body to science and become part of a "brave new future". Logan, however, finds the suit Hisako made him. Donning the mask, he tells Colcord that all that used to be true, but isn't anymore. By the time he's through, Omega Red is throughly disabled and Colcord is dead, bled out into the snow.
-Our heroes reunite and march towards home, although Fantomex opts to return to his free-wheeling independent life, with a promise to return to help out if needed. In the final scene, Armor leads Wolverine, in full costume, to Cyclops, asking where he signs up for duty.
POST CREDITS SCENE:
1) Another fun snippet of Wolverine adjusting to life as an X-Man
2) Agent Jackson brings everything she was able to salvage to a mysterious room full of futuristic computers and reports to a spectral AI that lives within them, labeled SINISTER. She regretfully informs him that the mutants were able to obtain some files from the site. We cut back to a shocked Logan openig up old Weapon X files on a computer.