Flashback
Logan stumbles out of a bar drunk. Little does he know he's being watched by a man in glasses. Logan chugs down the rest of his beer and drops it. He then notices the man in glasses. "What are you looking at?", Logan growls at the man and just then, two soldiers appear from out of nowhere, knock Logan out, and drag him into a van. The man takes his cell phone out and calls someone. "This is Professor Thornton. We found our test subject. Prepare the lab."
Fast forward
Logan is in a fluid filled cylinder with tubes inserted into his now naked body. Professor Thornton and several scientists look on with fascination. "Begin the adamantium bonding process.", says Professor Thornton to a lab technician. "Yes, professor. Commencing infusion." Something is pumped into Logan's body, causing him to bleed out of every hole. "His vitals are erratic but holding." "Excellent. Increase to maximum."
Fast forward
Logan is in a blizzard with a helmet on his head. He sees the infrared image of a grizzly bear. The scientists also see it through their monitors. "Weapon X's mental conditioning and reprogramming are at Stage 5. Begin combat assessment.", Professor Thornton says. As the bear stands up, Logan pops out his now metal claws and the two attack each other.
Fast forward
Professor Thornton and Sabretooth are walking down a hallway filled with test-tube babies. "I don't care how long you had him, Professor. This is a mistake.", Sabertooth says to Professor Thorton. "I know him. He can't be controlled. You have his DNA, so just let me kill him." "I'll take that under advisement, Sabretooth.", replies Professor Thorton and he walks away. Sabretooth growls in frustration, knowing full well that Thorton wouldn't even consider it. Little did either of them know, Logan had been listening.
Fast forward
Back inside his liquid tube, Logan is fighting his programing. "We are losing control! Increase the dosage!", yells Professor Thornton, "Initiate lock-down procedures and someone activate Sabretooth!" Logan manages to break out of the tube and then breaks into the room where Professor Thornton is in. Two guards storm in with guns loaded, but Logan takes them down, cutting off Professor Thornton's right hand in the process. Eventually, Logan manages to exit the Weapon X facility leaving a bunch of guards in ribbons. He then runs off into the Canadian wilderness.
Sometime later, Logan is still wandering through the wilderness naked and covered in blood, huffing and puffing his way through thick snow. Suddenly, a sound catches his attention. A loud howl, a cry of pain. Logan heads toward the sound and eventually comes upon the Hunter. His left leg is stuck in a bear trap. Without hesitation, Logan pops out his claws and breaks open the trap. The Hunter runs off on all fours, but not before turning his head to Logan and giving him a long look as if to say "thank you."
Logan wakes up to find Sabretooth punching him and that he is shackled to a wall in his underwear. "Wakey-wakey time.", says Sabretooth. "Logan, we missed you.", says Maverick, "Weapon X hasn't been the same without you. No one calls me 'bub' anymore. But I think out of all of us, Cyber's the one who missed you the most." Just then, Professor Thornton, who now has a clawed mechanical hand, and Cyber walk into the room. "One of these days I will crush your annoying skull, Nord.", growls Cyber. "He's very ashamed.", Maverick whispers to Logan. "Despite Maverick's idiocy Weapon X is indeed pleased to have you back, Logan.", says Professor Thornton, "We put considerable time and money into you. You were our best operative, Wolverine. So disappointing, but you did lead us to the Hunter in Darkness." "What do you want with the Hunter?", Logan snarls. "The same thing we wanted with you, Logan. A weapon.", replies Thornton. "I'll erase the Hunter's memories and reprogram him, just like I did you. And then, Weapon X will have the deadliest predator on the planet at our disposal." "You should've killed me when you had the chance.", growls Logan. "Because I'm gonna break out of here. I'm gonna kill all of them, and then I'm gonna cut your damn head off." Professor Thornton just smirks. "After I'm done with you, you won't even remember this conversation. I've erased your life before and I'm going to do it again." Sabretooth growls in frustration. He wants Wolverine dead. Professor Thornton, Sabretooth, and Cyber leave the room, leaving Logan alone with Maverick. "Oh Wolverine. You look so sad.", says Maverick. "Hey, if it makes you feel better, Lady Deathstrike tried to kill you while you were asleep." "Better than having to listen to you.", Logan retorts. "Man, does she hate you.", Maverick rambles, "I mean, we all hate you but Deathstrike really hates you. Hey, still have that unbreakable skull?" Before Logan can respond, Maverick takes out a gun and shoots Logan point-blank in the face. Everything fades to black.
Logan wakes up and finds himself trapped in a liquid filled tube. He then sees Lady Deathstrike on the outside glaring at him. "You will die today, Logan-san.", says Deathstrike as her finger scratches the glass. Logan bangs his fists against the glass, but it holds. "It does not matter what the professor says. These are your last breaths." Just then, Professor Thornton and Sabretooth walk in. "What are you doing here, Deathstrike? I'm about to start Wolverine's reprogramming.", says Thornton. "He has to die.", Deathstrike hisses. "How many times do I have to have this conversation with you? He's more valuable alive than…" Suddenly, Thornton collapses to the floor. There are deep scratches on his back. "Sorry, Professor. Gotta go with the lady on this one.", says Sabretooth as he wipes Thornton's blood off his claws. Lady Deathstrike claws the glass, causing it to break. Logan falls out and howls in pain as Deathstrike digs her fingers into his shoulder blades, relishing the sound of Logan's screams. Sabretooth then punches Logan and then restrains him. "Gotta love our healing factors.", Sabretooth says to Logan, "I'm gonna enjoy killing you for days. And then I think we'll drop the Hunter on a preschool or something. Just for fun." "Gaijin dog.", Deathstrike says to Logan, "For the dishonor you caused my family, you will suffer. And then you will die." "Sweetheart, both you and your honor can go to hell.", snarls Logan. Deathstrike becomes irate and throws her arm with full force. "Deathstrike, don't-!", cries Sabretooth but gets cut off as Deathstrike's arm goes through both Logan and himself. Seeing his chance, Logan headbutts Deathstrike and knocks Sabretooth out with one punch. Deathstrike comes at him fast, but Logan sees her coming. He dodges out of the way and with one swipe of his claws, cuts off her left mechanical arm. Logan then knocks Deathstrike out by kneeing her in the head. Logan then runs out of the room. Got to go find and free the Hunter. Can't let 'em turn him into a monster, like they tried to do to me.