Stornoway, fifty miles off the coast of Scotland. The X-Men are trying to get their hands on a hovercraft so they can see what’s happening on Dr. Moira MacTaggert’s research island. The owner of the hovercraft, Angus MacWhirter, refuses, however, because he made a deal with Dr. MacTaggert, not some "costumed freaks." Nightcrawler tries to make chitchat with the dockworkers, but they avoid him because of his "pointy ears an’ teeth." MacWhirter refuses to let the X-Men use the hovercraft and adds their money is forfeit for making a fraudulent reservation. Colossus doesn’t think this is very fair, proceeds to hang him on a hook and they take the hovercraft.
Banshee (who is leading, as Cyclops is still with the recovering Jean Grey) laments showing up at the dock in costume, as the confrontation could have been avoided with disguises. He is also worried about young Jamie Madrox (who takes care of the research station on Muir Island when Moira is away), who hasn’t been heard from for some time.
As the X-Men approach the island, it’s suddenly lit up "like a Scot’s Fourth O’ July." An instant later, a bolt of "eldritch fire" from the island causes the hovercraft to be pulled apart at the seams. The team swims to the island, and Nightcrawler observes that they always seem to crash. Wolverine calls it dumb luck, but then adds that it seems someone has it in for them. Banshee points out that the metal of the hovercraft seemed to come alive. Colossus mulls over the possibility of another fight to the death, but wouldn’t give up his new friends for anything.
The X-Men marvel at the size of the laboratory on the island, and Banshee wonders why Dr. MacTaggert would give all this up to be the "X-Men’s housekeeper." The X-Men go into action mode, and Colossus takes the point, but encounters some kind of force field. Wolverine checks on Colossus and Nightcrawler points out that they’re sitting ducks.
Suddenly, the ground lifts up and Banshee figures out that the force field is ripping the chunk of beach beneath them, out of the ground. It quickly hurls them towards the outer wall of Moira’s lab. A quick thinking Banshee gets the team to combine forces and punch through the wall to safety. Banshee speculates that only one man has all the powers necessary to do this to them. As if on cue, the doors to the room start to glow white hot and explode. Enter Magneto, who points out that they will all die here and he will become the Lord of All the World.
Meanwhile…a familiar aircraft lands at the landing pad behind the lab with Moira and a worried and angry Cyclops on board. Cyclops is upset that he has never heard of this "mutant research center." Moira points out that its purpose is to house dangerous mutants and to cure their hatred for humanity. Tthis project was begun when Xavier and MacTaggert were students together. Cyclops worries some of her "guests" might escape, but Moira doesn’t think that would happen. They find a hurt Jamie Madrox who tells Moira that she has only brought the X-Men here to be destroyed.
Jamie explains that this morning Polaris, Havok, and Erik the Red somehow got past all the automatic security and ambushed him. They went straight to the cell with baby Magneto and use a ray gun to grow him to an adult in moments. Magneto was furious about being turned into a baby, and he and Erik agreed to an alliance and a two-pronged attack on the X-Men.
Hearing this, Cyclops is freaked because while the New X-Men are good, they have never been trained to face Magneto. With a Magneto at full strength, they don’t have a chance. He tells Moira to take Jamie, get to the jet, and be ready to take off at any moment. He runs off to join the battle with Magneto.
Back at the Battle…the X-Men are getting pounded. Erik the Red has briefed Magneto on the new X-Men, and while Wolverine is confident, his metal skeleton soon gets him thrown through a wall. Colossus jumps to the aid of his friend, but Magneto points out how vulnerable he is because he is part metal. Magneto says he has never felt this good while Storm swoops in with a lightning bolt, but Magneto reflects it right back at her. Colossus knows that he would be safer in his human form, but useless in the fight, so he stays metal and throws a girder at Magneto, who deflects it easily and tosses Colossus out into the sea.
Nightcrawler ports out of the way of an attack, but Magneto can predict where he will appear with his magnetic powers, so Nightcrawler is buried in metal debris the moment he reappears. Banshee uses his sonic scream to shatter the floor under Magneto’s feet, but we learn that Magneto can fly. Banshee puts up a good fight, but Magneto encases him in a thin layer of metal essentially paralyzing him.
Magneto claims victory and marvels at his ability to take out this stronger team of X-Men so easily. However, Cyclops suddenly bursts in and hits him with an eye blast at full power. Cyclops surprises Magneto and is able to stun him, but still can’t penetrate the shields his foe erects. Cyclops realizes that with Erik the Red involved, this is about more than just Magneto vs. the X-Men.
Cyclops thinks that Professor Xavier might be in more danger than they are and orders a retreat. He rescues Banshee with a very narrow beam and orders the others to the jet. None of the X-Men are happy about leaving Magneto here, but Cyclops pulls rank and they all reluctantly follow. As they are retreating, Wolverine notices that Dragon-Fly has escaped. They find Colossus, and as they fly off Cyclops explains how Erik the Red is gunning for Professor Xavier, so they can’t waste time here with Magneto. Wolverine doesn’t buy it and says he won’t forgive Cyclops for making the X-Men look like cowards.
Back at Muir Magneto glories in his defeat of the X-Men, unaware that in the background Mutant X is waking…
Somewhere in space, on the command deck of the Starjammer:
A human man named Christopher, dressed in a futuristic buccaneer outfit and a huge reptile-like alien named Ch’od discuss that the nine stars are moving into alignment and that if the „Emperor" isn’t stopped from fulfilling his plan, it will mean the end of everything.
Eight thousand miles above the Atlantic:
Aboard a smaller starship the alien woman Lilandra arrives in Earth’s orbit, very low on fuel. She hopes she has enough to land. Unfortunately, that’s the least of her worries as she gets ambushed by her brother’s imperial cruiser and its photon torpedoes.
An apartment in Greenwich Village:
Professor X, Jean Grey, and her roommate Misty Knight welcome Jean Grey’s parents who are visiting. Outside the window, Polaris, Havok, and Erik the Red are watching while they plan their attack.