Things are tense in the New Mexico headquarters of the X-Men. Weapon X, just back from freeing Jean Grey from Sinister’s clutches, angrily threatens Magneto. Jean is trying to calm him, the other X-Men – especially Sabretooth – are ready for a fight. Weapon X snarls at Magneto that he and Jean are finished with the X-Men. Logan sacrificed his arm to save Jean, whereas the other X-Men on Magneto’s orders didn’t help with the rescue mission. Now he has enough of them. Jean asks Logan not to fight and to just leave with her. After Logan acquiesces, she telekinetically transports them away. Rogue offers Magneto a shoulder to cry on, but he brusquely turns away. Quicksilver offers to run after them and talk sense into them, but Magneto tells them that their decision is made. Jean telepathically contacts Magneto and asks him to forgive himself, as she has already done. She understands, why he acted the way he did, but she is leaving with Logan, because he needs her more than the X-Men do.
Meanwhile in the remains of Spokane, Washington, Holocaust, son of Apocalypse, surveys the ruined city, the handiwork of him and Apocalypse’s army. He is joined by his servant Wolverine – a ferocious hunter and killer – a product of the Dark Beast’s science – who until now has been busy butchering the city’s human population. Holocaust informs him about his next mission. He wants vengeance on Magneto, the man who is responsible for his dependence on his life support armor. He’s aware that Magneto is at a low point since two trusted X-Men have left him. Their conversation is disrupted by a grief-stricken human who attacks them for the murder of his family. Wolverine dispatches of him with terrifying ease and asks what he is supposed to do to Magneto. Find the person he’s closest to, kill that person and make Magneto watch, Holocaust, the murderer of Magneto’s daughter, tells him.
(several days later)
Magneto magnetically transports the X-Men to the ruined city of Denver, Colorado, in search of a bandit horde. Calmly he gives his orders. Rogue in the meantime is worried that he seems distracted, ever since Jean and Logan left. She’s afraid it’ll make him careless. Gambit tries to comfort her and decides that they’ll just have to stick close to him, just in case. Sabretooth has tracked the bandits to their hiding place. He believes that they are currently threatening some normals – the X-Men attack. Not exactly a hard job for the team and Sabretooth, Quicksilver and Iceman banter back and forth. Magneto angrily interrupts and orders them to treat this as a real battle, like Weapon-X and Jean no doubt would have. Hearing this Rogue and Gambit worry even more.
Two criminals watch the battle from afar, wondering if they should join in and unaware that they in turn are watched by Wolverine. The killer catches and changes them, increasing their strength, awakening bloodlust in them and siccing them on the X-Men. The two attack and while Rogue and Gambit manage to stop them, one of the duo throws a non-metallic knife at Magneto, hitting him in the shoulder. Gambit takes charge, keeps Magneto from keeling over and orders a retreat, despite Magneto’s protests. Wolverine is left to wonder : he had assumed that the closest one to Magneto would be his son Quicksilver, but apparently Rogue and Gambit are even closer to the man. He calls out the other bandits and schemes.
Back at the X-Men’s headquarters, Storm bandages Magneto and asks him to take it easy. Magneto is being a lousy patient and chides the X-Men and especially Gambit for being undisciplined. Quicksilver plays the voice of reason and points out that after all they saved the humans as they planned to. Their mission was accomplished. Gambit urges Magneto to rest and reminds him that he was the one to awaken Gambit to the dream in the first place. Then he asks Rogue to come out him for some downtime. Rogue refuses, telling him she has to go over next week’s plans with Erik. Gambit takes this rebuttal in good humor, but reminds her that he has to talk with her about something very important soon.
At the same time in Denver, disappointed in the way his human agents failed him, Wolverine dispatches of a rather loud-mouthed one. Then, he tells them that they will take the fight to the X-Men.
In New Mexico, Iceman teases Gambit about his relationship with Rogue. When he notices how serious Gambit is about her, he asks how Gambit will handle the physical problems between them. Gambit replies that Magneto is working on a means to help Rogue control her powers, so he isn’t worried. Iceman presses whether Rogue actually knows about the depth of Gambit ‘s feelings and Gambit admits he isn’t sure. Elsewhere in the compound Rogue asks Magneto to go easy on himself. He is driven to act as long as Apocalypse butchers people and he is eaten by doubts, as he feels he cannot even keep his team together. Rogue props him up, and tells him that at least she will stay with him forever. The two exchange a look, fraught with meaning and a confused Rogue quickly leaves.
By then, Wolverine and his horde of followers have reached the Rocky Mountains. Wolverine finally get the X-Men’s scent and now knows the way to their base.
(a short time later)
Within that base, Rogue interrupts Quicksilver’s speed-reading. They reminisce about Pietro’s dead sister Wanda and Pietro admits to Rogue how glad he is that she was with his sister when she died. Rogue asks him what Wanda would have thought about Magneto making her second-in-command instead of his son. Pietro tells her he has no problems with that and since the team is likely to expand soon anyway, they’ll need more than one leader soon. Gambit interrupts them and tells Rogue that he wants a commitment. She tells him she’s sorry and runs away. Quicksilver suggests the confused Cajun better have a talk with Magneto, who’s training outside. Magneto is indeed up again training with Storm, Colossus and Sabretooth, urging them to give no quarter, to show no weakness. Gambit interrupts the session, asking Magneto to talk with him. Magneto impatiently tells him to either join the training session or shut up.
Outside the compound, Wolverine and his troops have arrived. An especially overzealous human wants to attack, but Wolverine breaks his neck and asks the others to listen to his plan.
The X-Men have finished their workout, but Sabretooth is spoiling for some more action. Magneto tells him that they’ll start a new mission early the next day. Gambit approaches Erik again, asking him about Rogue. Magneto tries to evade the subject when both are interrupted by the lady in question who asks Remy to leave as she needs to speak with Magneto privately. Rogue tells Magneto she’s confused about her feelings for him. Magneto seemingly changes the subject and tells her he has found a way to solve her power-problem. He erects a biomagnetic shield around his body and offers her his bare hand. She takes it into her own bare hand and realizes that she is not absorbing his consciousness. Rogue starts crying and Magneto touches her face to comfort her. The two move closer, unaware that Gambit has secretly been watching everything.
Furiously, he attacks Magneto, feeling betrayed. Then he bitterly snaps at Rogue that she didn’t have to start a relationship with Magneto just because she promised his daughter on her deathbed she’d take care of him. Enraged by that unfair accusation, Rogue slaps him. The three are literally saved by the bell, as the alarm rings – the front gate’s been breached. The X-Men are already in battle against the enhanced humans and seem dangerously overconfident. Magneto, still distracted by what happened, doesn’t notice Wolverine closing in on him until it’s too late – the villains strikes him down. He then proceeds to attack Rogue, but is stopped by Gambit, who jumps at him. The weakened Magneto tries to join in, but Wolverine takes the stunned Rogue hostage and orders the two men to stand in a corner.
Rogue becomes conscious again, sees them in danger and acts on instinct. She grabs Magneto and flies him to safety. An amused Wolverine smashes the wall around Remy, burying him under the bricks. In the meantime, the other X-Men have noticed him and attack him together – to no avail: Wolverine is the only one left standing. He tells Rogue if she lets him kill her while Magneto watches, he’ll let him live. Gambit, who has dug himself out again, seemingly punches him in the back. As Wolverine mocks his feeble attack, he notices that Gambit actually put a kinetically charged-up rock into his belt. The results are explosive and very final for Wolverine. Rogue tells Remy she didn’t want to hurt him, but Remy cuts her off. All his life he pretended to be a loner, then he found someone he loved, and, of course, she loved someone else. Just his luck, he tells her and leaves the X-Men.