Clad in his red and purple costume, Magneto is sitting on a throne and gazes into a crystal orb connected to the huge machine in front of him. It displays a vision of a funeral; the X-Men in their civilian identities are paying their final respect to their late mentor, Charles Xavier. Magneto rises from his chair and gestures angrily as he states that his only regret is that is was someone else and not he himself who killed his hated enemy, Charles Xavier. Thinking this to be the perfect time to strike against the X-Men, Magneto calls for Quicksilver, who doesn’t respond.
Meanwhile, at the funeral, one Reverend Brown describes Xavier as a good and just man who has lived a life apart and dedicated his days to the welfare of other. Scott Summers thinks to himself that the reverend is referring to the good that Xavier did as a teacher, and that only a handful of people know the full extent of how the professor protected humanity. The five students of Xavier’s School for Gifted Youngsters are the only attendants at the funeral and, as the reverend continues the service, they are all lost in their thoughts. While the others are still in shock about what happened, Scott already thinks about the mission they have inherited – to defend the world against evil mutants. While he hopes that the X-Men will be able to live up to Xavier’s expectations, he comforts Jean Grey, who is shaking and about to cry.
In a nearby town, several people don’t quite believe their eyes, when a blurry figure passes right through them. They see that it is a man, though moving faster than an express train. The young man known as Quicksilver runs even faster and in no time, he has reached the graveyard, where he tries to stay out of sight so that the X-Men won’t notice him.
It’s raining at the funeral, and Hank McCoy is thinking about the many battles that the professor led them into, when Warren and Bobby spot Quicksilver and alert their teammates. The X-Men have heard about the mutant speedster having quit the Avengers and rejoined Magneto, but they never would have expected him to show up here. Thinking that he has come either to gloat or to attack, the five teenagers cross the short distance to their fellow mutant. Quicksilver is leaning against a tree, rather exhausted from his run. As he sees the X-Men approach, he prepares to leave again, though Scott pleads with him to stay and talk.
Pietro thinks to himself that, when he obeyed to his impulse to attend Xavier’s funeral, he knew they might see him, and he even wonders if subconsciously he wanted to be seen, in order to end the loneliness he experiences ever since turning his back on humanity. The X-Men’s leader asks Quicksilver why he has come, and slowly moves closer to him, wanting to make sure that Reverend Brown can’t overhear their conversation as it might compromise their secret identities. Quicksilver notices that Scott is edging nearer and perceives this as an attempt to lull him in with some nice words only to get close enough to capture him. He zooms away as quickly as he came, reassured that his place is with the Brotherhood as there is nobody, save Magneto, that he can trust.
The students of Xavier’s are left puzzled; they can’t make any sense of Quicksilver’s behavior. By now, Reverend Brown has caught up with the five teenagers and reminds them of the ceremony that needs to be finished. Scott is relieved that the reverend hasn’t seen Pietro run off, and makes up an excuse, explaining that they thought somebody they knew. From afar, Magneto is still observing the events at the graveyard, and is even more outraged than before. Quicksilver went to the funeral without notice or permission – possibly with the intent to betray him. Though pay he must, the master of magnetism declares, it makes no difference in the long run. With or without the speedster, he will soon destroy the X-Men.
As soon as the five X-Men return home, they take off their coats and suits, revealing their colorful costumes underneath. Still thinking about the funeral, Hank says that he wishes more of Xavier’s friends could have attended. However, Jean reminds him that FBI agent Fred Duncan dared not to come, to avoid people wondering what sort of connection he had with the professor, and the Banshee was away on a mission and could not be reached. Cyclops is sure that they were with them in spirit though, before announcing that there is something he must do.
Apparently, Professor Xavier told him to press a certain button hidden behind a painting in case of his death. As soon as he presses it, a cleverly concealed panel in a nearby wall opens, revealing a huge projector. The lights dim down automatically, and the X-Men sit down on the chairs, as the professor’s sad face appears on a lowered screen before them. “Listen, my X-Men, to this message I’ve prepared for you to hear… after my death! I’ve so much to say… and a final request to make of you… and so little time… so little time!” While the X-Men are still in shock, trying to adjust to the idea that they are hearing the professor’s voice for the final time, the recorded message continues.
“For the past few weeks, I have known that I was dying…,” Xavier says, “… dying of a disease which neither medical science nor my own mutant powers can cure! Therefore, I have been attempting to complete the final stages of your training… so that you may carry on when I am… gone!” Iceman understands that this is why the professor was driving them so hard in the past few days, and Beast agrees. In fact, he blames himself for not suspecting the reason for Xavier’s recent behavior. Cyclops orders his teammates to be quiet, as they have to hear every word of the message. Marvel Girl is in tears; she turns away from the screen and covers her face with her hands.
“Moreover, so that my mental powers may not be entirely lost to you, I have been secretly preparing Jean Grey! By now, she should have added telepathy to her mind-over-matter abilities!” Hearing this, Angel remembers how he thought that Jean and the professor did care about the team anymore, when actually he was training her to take over some of his own powers. “For, if my calculations are correct, you’ll soon be called upon to face one of the greatest mutant menaces of all! It is my belief that Magneto has returned to Earth!!” One of the X-Men exclaims that he was right, but that the film must have been made before even the Avengers knew of Magneto’s escape.
“And now, I’ve no time left… for I have just learned the location of the sinister Sub-Human known as Grotesk, and must try to stop him before he destroys the entire planet! If I fail… or if I should perish in my attempt… this brief film will say what I myself could not! And now, farewell, my X-Men! The torch has been passed… and I know you shall be worthy of it!” Now, the Beast too wipes a tear from his eye, whereas Jean is in denial and says that this can’t be the end. Referring to their mentor’s final words, Hank answers that it won’t be, as they will carry on and make a new beginning.
Somewhere in the Atlantic, there’s a fortress located on an unknown, rockbound island. In its center, there’s some strange device in the shape of a huge, metallic sphere that dwarfs the surrounding buildings. Magneto stands on a high point of the island, demonstrating his vast magnetic powers as he wrecks a nearby cargo ship with a mere gesture, pulling it onto the rocks. As he does so, Magneto states that it would be beneath him to scrounge for supplies when he can so easily obtain them from his inferiors, the Homo sapiens. After letting the ship’s crew escape, so that they can tell mankind of his glory, Magneto blasts the ship’s remains apart. He then heads towards his fortress, to prepare himself for Quicksilver’s return.
At precisely that instant, a magnetically-power vessel approaches the fortress from a different direction, carrying Quicksilver. Unaware that his earlier actions have been witnessed by Magneto, he thinks to himself that his destiny now lies on this isolated island, far away from his life as an Avenger, but also a safe distance from humanity’s ever increasing fear of mutants. Having landed the craft, Pietro sneaks silently into the fortress, his first concern being his sister, Wanda. He wants to check on her to see if she is any better since he left, when suddenly he notices someone lurking in the shadows.
It’s the Toad, who was cowering behind some crates. Having been spotted by his supposed teammate, the Toad leaves his hiding spot, declaring that he is the most loyal ally of Magneto, who sure might be interested in Quicksilver’s silent entrance. As the Toad hops away, Quicksilver tells him to report what he wants, as he is not Magneto’s mere lackey like him, and he can go where he wishes. Looking back, the Toad repeats that he will tell everything to Magneto, and that he will punish Quicksilver for his insolence.
Once the hopping mutant is out of sight, Pietro proceeds to Wanda’s room, and finds her condition to have improved somewhat – outwardly, she seems better, but he can tell that her thoughts are vague and her hex power is still gone. He briefly thinks of the Avengers and wonders if they could help, when Wanda hugs him and tells him that she searched for him and was worried when she couldn’t find him. She even calls herself a burden to her brother and admits that she considered the possibility of he having left her forever, though Pietro assures her that he will never leave her. The next second, though, the strain of the previous hours and his many concerns take their toll on Pietro, and he collapses to the ground. Now it’s Wanda’s turn, to provide some comfort, as Quicksilver tells her how he had hoped Charles Xavier might be able to cure her, but that he arrived too late and the X-Men’s mentor was dead.
At this point, Magneto angrily bursts into the room, asking whether Pietro really would think that any living being could enter or leave the island without his knowledge. The Toad, hot on his heels, he urges his master to teach Quicksilver a lesson for threatening his only loyal servant earlier on. However, Magneto strikes at the Toad instead, lifting him into the air by the metallic belt he forces the Toad to wear all the time. While the Toad begs to be put down again, Magneto explains that it is for Magneto alone to decide how he deals with those who betray him. With growing concern, Quicksilver notices that their leader is becoming more cruel and more powerful each day, and states that he has not betrayed Magneto.
The self-declared master lets the Toad drop down without warning, as he angrily turns towards Pietro and accuses him of lying straight to his face, as he has witnessed him leaving the island and attending Xavier’s funeral. Quicksilver calmly explains that he only went there out of sadness for the fate of a fellow mutant, one who understood what it meant to be an outcast. Calling Quicksilver a fool, Magneto asks if he isn’t able to sympathize as well. Why does he have to turn to “that human-loving traitor,” when it was he who once saved the twins from an angry mob? When it was he who works night and day to create a device capable of restoring the Scarlet Witch’s powers? Pietro replies that he hasn’t seen any proof of this, earning him another warning from Magneto, who ends the argument now, lest he forgets their “long-standing friendship.”
Next, Magneto explains that, in a few days, a cargo ship carrying invaluable equipment will pass the island. Once he possesses that equipment, he can finish the device he spoke of. The Toad suggests for he and Magneto to leave now, but his master pushes him away, asking if he has to be forever beneath his feet. Wanda whispers to Pietro that she doesn’t trust Magneto and that they should leave. Pietro, however, says that can’t, at least not yet. Having left the room, Magneto thinks to himself that both Wanda and Pietro suspect his true intentions, but that they haven’t realized that it was he who caused the human’s bullet to grace Wanda’s head, so that they would join him. And, soon, once his secret plan will be accomplished, he will no longer need them or anyone else.
(a few days later)
Standing atop his fortress, Magneto spots the cargo ship he has been waiting for, apparently it’s carrying a giant new computer that he needs for his plans. Pointing his finger at the vessel, he stops it right in its track. Aboard, there’s a commotion, only five people are not really surprised by what’s happening. It’s the X-Men in their civilian identities. They are aboard as Scott Summers correctly deduced that Magneto couldn’t resist the scientific equipment the ship is transporting. A deck below, a crewman tries to radio for help but it’s no use. The radio has gone dead. Suddenly, the entire ship is being lifted into the air, much to the shock of the crewmen on deck, who are now able to see the huge fortress on the nearby island.
Meanwhile, the X-Men have changed into their costumes, and prepared themselves to leave the ship. As they make their way to the deck, Angels says that they were lucky his parents had just sent him his monthly allowance, or else they would have been able to book a passage on this cargo ship. The Beast comments that it was quite more than a mere “allowance,” for a small sum more they surely could have bought the entire vessel. Iceman creates an ice-ramp so that he and his teammates can get to the island below. Flying by his leader’s side, Angel asks Cyclops how he figured out that Magneto was likely to stop this particular freighter. Scott explains that it was a calculated risk, based on the cargoes of the last few ships that disappeared in the area.
Inside his fortress, Magneto curses as he observes the X-Men’s arrival on a computer screen. He didn’t want this final showdown to occur that soon, as he would have preferred to plan their downfall carefully. Actually, the computer on the ship was the last thing needed to complete a machine that shall bring him mastery over the entire planet, by enslaving the minds of all Homo sapiens. Then, isolated and alone, the X-Men would have been defeated quite easily. On the other hand, Magneto declares that there’s no reason for regret, as the five mutant teenager only hasten their doom if they attack now, for there is no way they could beat him.
The X-Men make their way through the fortress, and soon have reached it’s inner sanctum, prompting Marvel Girl to say that she doesn’t like it, as they have gotten this far way too easily. The Beast agrees, and Cyclops suggests that facing Magneto in a large open area like the one ahead of them might be their best chance. In fact, Magneto is rapidly approaching this area from the opposite direction, with the Toad again hopping by his side and asking what special traps his master has laid out for the X-Men. Magneto days he has no need for traps, as he sure has enough power to defeat his foes in a fight. Indeed, in the next instant, he manipulates a loose part of the ceiling and slams it into Angel and Marvel Girl, to dispose of them.
The Beast calls Magneto a coward for still letting the metal do his work for him, rather than engage them in a hand to hand combat. Next, he leaps against a huge stone urn, making it topple towards Magneto, who reminds the agile X-Man that even non-metallic objects contain enough iron atoms for him to affect. That said, he causes the stone urn to explode right in front of Hank.
As Jean and Warren come around and try to get up, they notice an emerald blur in the room, approaching Cyclops. The X-Men’s leader immediately realizes that it’s Quicksilver, and says that he hoped he would not attack them, which is why he refrains from using his optic blast and tries to get him with his fists. Pietro doesn’t have such reservations, though. He attacks with his full speed, though only because he secretly hopes to subdue the X-Men himself, so that they won’t be harmed by Magneto. However, Magneto doesn’t let the speedster handle the situation all by himself, and magnetically tears apart the floor under Cyclops’ feet to make him stumble.
Cowering in a corner, the Toad activates a huge battering ram, knocking over four of the X-Men. Before it can hit Cyclops, however, the X-Men’s leader blasts the device apart with his optic beam. Still this small victory doesn’t him any good, for now all five X-Men are standing in the area where magneto wanted to have them. He pushes a lever, turning the very floor of that section into an electric field. As the five mutants are rendered unconscious, Magneto raises his fists. He has defeated the X-Men... “for the final time.”