The Boundary Waters National Wilderness area, in Canada, where the stillness of dawn is disturbed by the sound of rustling leaves. Logan a.k.a. Wolverine of the X-Men appears, claws at the ready, as a deer approaches him. 'Don't gimme the helpless, innocent look, kid! It ain't gonna help ya!' Wolverine snarls at the deer, warning it that with just one swipe of his claws, it will all be over. But Logan doesn't use his claws on the deer – instead, he slices apart a root that one of the deer's ankles had become tangled in. 'You can go scampering off to McDonald's for breakfast' Logan jokes. Logan thinks that the deer is a lively little cottontail without a care in the world, when suddenly, he hears a rumbling sound. He spins around, as a man in a white and red costume that resembles the Canadian flag bursts upwards, and knocks Logan aside. 'It's been a long time, little man!' the new arrival exclaims.
'Vindicator!' Wolverine calls out, asking him what he is doing here, and explaining that he got a message that Heather had to see him and that it was life and death. Vindicator circles around and flies in front of Wolverine, telling him that he may have deserted their team to work for Xavier, but that he belongs here. 'I've come to take you back!' Vindicator announces. 'In a pig's eye, Bub' Wolverine responds, leaping aside to dodge an electro-magnetic blast that Vindicator fires at him, telling him that he has to be faster than that, and that he is practically posing. 'Your speed hasn't slipped a notch, Wolverine' a voice calls out, and Wolverine turns to see three others standing nearby – a large furry being, a short man and a man in a green and brown costume. 'So, ya brought the whole flee club along fer the sing-along, huh, Vindicator?' Wolverine mutters, acknowledging Sasquatch, Puck and Shaman.
Wolverine tells them all to get it through their thick skulls – he is never coming back to Alpha Flight. 'You shouldn't be takin' that tone of voice with yer old buddies, eh?' Puck calls out as he cartwheels towards Wolverine, who turns to the diminutive man and reminds him that he tried that trick a hundred times when they trained together. 'An' it never once worked!' Wolverine remarks as he slams into Puck, knocking him backwards – before he quickly turns around to where Sasquatch has raised a large boulder overhead, and slices his claws through the boulder while remarking 'You weren't really thinking of dropping that rock on my head, were ya, Sasquatch?' and pointing out that Sasquatch might have pounded him down to Puck's size – and they all know that little squirt isn't doing much for Alpha Flight's image. The shrapnel that is created by Wolverine cutting the boulder apart sprays backwards into Sasquatch's eyes, blinding him with the rock fragments. 'Wait'll I get my paws on you, Logan!' Sasquatch calls out.
Wolverine suddenly finds himself unable to move, and looking down discovers that vines are creeping up his legs. 'Only one guy can do that trick – Shaman!' Wolverine snarls, as Shaman approaches him and points out that he must be rendered immobile so that they may speak. The vines move up Wolverine's legs and chest, as Logan struggles to break free, he exclaims 'Guess I didn’t make myself clear the first time, Medicine Man! I ain't interested in anything ya got to say!' With that, he shreds the vines apart with his claws. 'Got it, longhair!?' Wolverine asks as he flings one of the thick vine segments at Shaman's face, knocking him backwards.
'Guess ya ran outta tricks, Alpha Bits! Now, I'll be taking my -' Wolverine begins, when suddenly, he finds himself carried upwards into the air, by Northstar and Aurora! Northstar smiles and tells Wolverine not to struggle, as Aurora asks 'You would not want us to drop you from such a height, would you?' Wolverine just thanks them for he lift, and uses his strength to slam the twins into each other, joking that he hates to be a burden on friends. 'And don't ferget to write!' Logan exclaims as he falls from the dazed twins, towards the forest below. He knows that he has to angle his descent and hit the branches just right, or else he will be swallowing pine cones by the bunch!
Wolverine lands safely in one of the trees, and watches as Northstar and Aurora rejoin their teammates on the ground. Northstar reports that there is no trace of Wolverine. Vindicator points out that Wolverine must be nearby, and instructs his teammates to fan out and find Logan as the lab is expecting them. 'Real pleasant' Wolverine frowns, as his mind wanders backwards to the lab - although it looked more like a fortress from the outside.
'Doctor Cornelius, how is our patient?' a bald man in a long green coat asks as he walks towards a stasis tank in the center of the laboratory, where a hairy, muscular man floats in the tank, a strange helmet covering his head. Doctor Cornelius sits at some monitors and addresses the bald man as Professor, and tells him that their patient could be better, that he put up some resistance when their boys picked him up last night – but he is not damaged goods. The Professor instructs Doctor Cornelius to continue the adamantium feed, as he sees the suffusion enacting, and the metal bands are being absorbed. The Professor watches as Dr Cornelius reports that the feed is impeded – that their patient is resisting the adamantium, so he adjusts the feed accordingly, and while they are compensating, he has never seen anything like the resistance the patient is putting up. Eventually, the adamantium reservoirs are drained, and the absorption process is complete. 'And our dear Logan?' the Professor grins, as the strange helmet is raised up off Logan's face. Why not ask him yourself?' Dr Cornelius suggests.
'Excellent idea!' the Professor smiles, before informing Logan that his skeleton has been infused with a rare metal called adamantium, virtually indestructible, meaning his bones should now be unbreakable. The Professor tells Logan that he should be proud, as he is the first, and they hope to make use of his gifts. 'Have nothing to say?' the Professor asks. Inside the tank, Logan remains silent as he realizes that there is an itching in his arms – it starts to drive him crazy, when suddenly – metal claws burst through his knuckles! 'What's happening?' the wide-eyed Logan wonders, while the Professor thinks to himself that this is extraordinary – and quite unexpected. 'Those claws!' he tells himself, before realizing that this explains why so much of the adamantium seemed drawn to Logan's wrist area.
Suddenly, Logan uses his claws to break open the tank he is trapped int. 'Stop him! He's breaking free!' the Professor calls out, while Logan rushes through the lab, knocking aside two guards in purple and yellow costumes. 'Security! Stop that animal before it escapes! Secure every exit!' Dr Cornelius shouts over an intercom, while the Professor watches as Logan begins tearing apart some machinery. The Professor is concerned that if Logan rips out the machinery it might cause an explosion, and suddenly, a panel slams down in front of Logan – but the damage he did to the machinery was enough to create that explosion, which tears open a hole in the side of the laboratory. Logan leaps through the hole in the laboratory out into the snow-covered wilderness. He makes his way into a forest, and howls as the laboratory explodes behind him.
'No more labs – ever!' Logan thinks to himself as he perches in the tree, when suddenly, the tree begins to shake, and he falls to the ground, courtesy of Shaman. Shaman stands over Logan and tells him that there is no escape – he is theirs. 'I'll say it fer the cheap seats... I ain't -' Logan begins, before Vindicator blasts him with a surge of electro-magnetic energy. Logan frowns and boasts that it is going to take more than some pantywaist burst to take him out. 'C'mon, gimme yer best shot!' Logan exclaims – so Sasquatch slams his fist into Logan, taking him by surprise and enabling Puck to put restraints around Logan's arms, neck and ankels. Puck tells Vindicator that Wolverine is secure, and that these shackles can hold a raging bull. Vindicator stands smugly in front of Logan, who declares 'Ya know I ain't gonna work for ya, Vindicator. Whatta ya want me for?' Vindicator reveals that they don't want him – only the secret he keeps inside of him.
A thousand miles south, at Professor Xavier's School for Gifted Youngsters, Scott Summers a.k.a. Cyclops, Remy LeBeau a.k.a. Gambit, Rogue and Hank McCoy a.k.a. Beast gather around Jean Grey who is using Cerebro. Gambit asks her if she has had any luck finding the old man, but Cyclops tells Gambit to be quiet, for if Jean is to locate the Professor she will need to maintain absolute concentration. Jean tells Scott that it is all right, and that even with her telepathic powers amplified by Cerebro, she is still not getting the slightest readings. Jean removes the Cerebro helmet and stands up, announcing that it is as if the Professor has disappeared from the face of the Earth!
Indeed, Charles Xavier and his arch enemy Magneto were duped into journeying to Antarctica, where an avalanche dropped them into a steaming jungle, miles below the surface. Crossing a long swing bridge, Charles thinks he sees a woman on the other side of the bridge. 'Perhaps she may help us' Charles suggests, before calling out to the woman, 'Who are you?' he asks her. The woman has greenish-white hair and wears a skimpy, psychedelic dress as she approaches the men and introduces herself as Vertigo. She then declares that all the Mutates of the Savage Land are Magneto's creation, but that they have turned against him. Before either Magneto or Xavier can respond to that comment, Vertigo tells them to enjoy this bit of disequilibrium which she saved up just for them.
Both men stagger, before Charles, dizzy and unable to stand, topples over the side of the swing bridge. Magneto reaches out and grabs Charles, preventing him plummeting to certain doom. Magneto holds up a sharp rock with his free hand, and declares that as they have lost their powers, there is only one way to prevent further assault. He then uses the rock to cut through the rope that holds the swing bridge together. 'We must escape – any way possible!' Magneto exclaims as the half of the bridge he is clinging to breaks away, with both sides of the bridge falling back towards the cliff they are each connected to. Magneto and Xavier are able to drop down onto a ledge near where their part of the bridge lands. 'Though every fiber of my being rebels at this...' Magneto utters, to which Charles presumes he would have preferred death. Vertigo, meanwhile, clings to the bridge part that she was on, and watches as Charles and Magneto run along the ledge, and she tells Magneto not to think that he has gotten away, and like the song says – they have only just begun to live – and kill! Magneto tells Vertigo to be quiet, and warns her that all of them will pay for this indignity.
On the other side of the world, back in Canada, specifically a high-tech lab complex, where Vindicator – whose real name is James MacDonald Hudson – readies his unwilling captive. Logan is strapped to a table in the middle of the lab, and Logan tells Vindicator to give him the scoop. 'What's this all about? We were friends once. If that means anything to you, Jim...' his voice trails off, as Vindicator tells Wolverine that he is sorry, but he is not at libety to discuss that, because he is not in charge here. 'That's right. I am' a woman with red hair and glasses announces as she enters the lab. The woman informs Wolverine that they traced his movements when he crossed into Canada, and they realized their plan to return him had worked. 'Heather!' Wolverine gasps as he sees the woman. 'You sent the Alpha-Bits after me! You set me up!' Wolverine snarls. Heather claims that she had no choice, to which Wolverine tells her that there is always a choice. 'Isn't that what you told me... years ago?' Logan remarks.
Logan had made his break from the Professor, on the run, hungry and howling, half out of his mind and in pain. He suddenly encountered James and Heather Hudson who were in the wilderness doing research. 'Let him go or I'll shoot!' Heather shouted, raising a rifle as Logan was on top of James. Heather fires – the tranqs, meant for a deer, struck Logan in the shoulder. Scientific curiosity takes the better of the Hudsons, who take Logan back to their cabin for observation. Strapped to a bed, Logan has no intention of staying put, and roared as he freed himself from the restraints. He has had enough of being bound and helpless – it was payback time. Without even knowing it, his new claws just pop out, as he backed Heather into a corner. She begs him not to her hurt, and explains that they only wanted to help him. Something in Heather's voice gets the better of Logan, who drops to the floor, 'Why did they do this? Why?' Logan asks. Heather puts her arms around Logan and tells him that it is going to be okay, that it is all right.
In the weeks that followed, Heather keeps her promise, nursing Logan back to health, making him feel almost human again. Almost. Sometimes the turmoil inside of him would become too much, and Logan would lose it – but Heather and Jim would be there with soothing words and hands, and Logan would pull back. A couple of months pass, and Logan begins to feel like he has it all together – but the Hudsons weren't prepared to let go of him, and told him that they had some friends in the government who might have a place for him – and Logan likes this proposal.
Logan was introduced to a friend of the Hudsons – General Chasen – the government liaison to Department H. Logan is officially “hired”, and saw Jim in his Vindicator for the first time, before he is given a package – that is when Logan realizes that the Hudsons were important people, and he was ready to join the crusade. Inside the package was a blue and yellow costume, and it fit him like he was born to wear it. He didn't like his codename, though – Weapon X. Logan was now officially part of Department H and its enforcement arm – Alpha Flight – ready to do it all for God and country. He notices the approval in Heather's eyes when she saw him in his costume, and Logan feels something strong inside.
After recounting these events to Heather, Logan is greeted with another surprise, as General Chasen enters the laboratory, announcing that he is certain Logan will be feeling something quite strong inside him again – though it might not be what he desires. Heather greets General Chasen, who tells Logan that since his defection, they have repeatedly tried, unsuccessfully, to duplicate the process that created his adamantium skeleton, and thereby creating new indestructible agents, which is why they decided to lure him back and conduct experiments on him to determine how he survived the bonding process – and this is the only way to do it. 'So that's what this set-up is all about. Well, I could o' saved you some trouble, Chasen. I survived 'cause I'm a mutant. I heal fast, dimwit' Logan replies, to which Chasen replies that there is only one way they can be absolutely sure. He c Heather to begin, and a laser blasts down from some equipment positioned above the table where Wolverine is restrained.
The laser blasts into Wolverine, who screams, while Heather looks shocked and exclaims 'You told me he wouldn't suffer this time! It's the only reason I agreed to help!' but General Chasen tells Heather that they don't have time to be gentle, and instructs her to continue the laser probe. 'No!' Heather retorts, pointing out that the proper precautions were not taken, she declares that this is outrageous. 'The only thing outrageous here, lady, is your conduct! Consider yourself on report! Any further lip and -' Chasen begins, pointing at Heather, who warns him not to threaten her. 'EVER!' Heather shouts as she smashes a stool into the computer console. 'Stop!' Vindicator calls out, and with everyone else occupied, Wolverine uses this chance to work on the shackles, which start to come loose. 'Now you listen to me, General. You may be in charge – but don't you ever talk to my wife that way again!' Vindicator declares, to which Chasen points out that this arguing is getting them nowhere.
'This ain't strictly true, soldier! Gave me the seconds I needed to do this!' Logan calls out as he breaks free of the shackles restraining him, to Chasen's horror. Chasen begins to run out of the lab and orders some guards to seize Wolverine, but Logan knocks the guards aside with ease and tells Chasen that he is slipping if he thinks these tinker-toy robots are the best he has to throw at him. Vindicator suddenly drops down between Wolverine and Chasen, and tells Wolverine that that is enough, and that he is not getting past him. 'My force field is on!' Vindicator adds. 'I know what you've been through – just try to -' Vindicator begins, but Logan tells him that he doesn't know jack. 'And here's what I think o' yer crummy force field!' Logan shouts as he grabs Vindicator and hurls him across the lab into some monitors.
'Yer one o' the culprits, Jimmy boy! I got a good mind to -' Logan begins as he grabs Vindicator by costume and raises his claws overhead. 'No! Logan – don't!' Heather calls out. 'He's my husband! Don't hurt him – please!' Heather pleads. Suddenly, some of the machinery in the lab explodes, and a hole is created in the wall of the lab. Logan looks up from Vindicator to the hole and remarks that this is his cue to leave. He tells Heather not to worry, that her husband will be fine. 'The big stiff's just stunned' he adds. Heather tells Logan that she is truly sorry, and assures him that she had no idea Chasen would go this far. Logan looks at Heather and tells her that Chasen isn't the one who put the most hurt on him – if she understands what he is saying.
Logan then tells Heather that if they ever meet again, it will be on his terms – period. Heather responds by telling Logan that she doesn't blame him for feeling this way, and bids him goodbye. As Logan leaps through the hole in the lab, he suggests to Heather that she tell the rest of Alpha Flight that he is still an ex-member – permanently. Wolverine trudges off through the snow, while in the lab, Heather goes to Vindicator, who asks if it was so wrong to want him back in the group – as they are like family to him. 'Right?' Vindicator asks. Heather tells her husband not to be blind, and that whatever part of Logan they had, it was lost long ago. She points out that they tried to cage something that despises captivity, and that they were fools for ever trying. Heather hopes to God that Logan can forgive them.