Ever since the funeral of their mentor, the five students of Xavier’s school have had no time to comprehend the full effect of their teacher’s death, as they were too busy fighting Magneto and his Brotherhood of Evil Mutants. However, now with the master of magnetism apparently dead, the five grieving teenagers have gathered around Xavier’s gravestone, each of them lost in their own thoughts. Hank McCoy finds himself unable to imagine a life without the professor. Warren Worthington thinks back to the X-Men’s battle with Magneto, during which the X-Men made use of the many things that Xavier had taught them, making it seem as if he was still among them. Scott Summers feels the heavy burden of leadership on his shoulders, as the professor named him deputy leader of the group. “He was so young... and so good,” Jean Grey thinks, recalling that weeks ago Xavier told her he was dying. Still, she keeps praying that all of this is nothing else but a horrible dream from which she will wake up soon.
The five teenagers believe themselves to be the only ones on the lonely cemetery, when their silent mourning is suddenly interrupted by a voice behind them. The man apologizes for intruding at a time like this, but he needs to talk to them about some pressing matter that can not wait. A bit startled, Jean asks who he is and what he wants, while Hank tells the man that they wish to be left alone. However, Scott holds him back, saying that he recognizes the visitor, who then introduces himself to the others as Amos Duncan, FBI.
After stating that he expected Scott to recognize him, he asks where they could talk, once more mentioning that it is urgent. Scott suggests that they had back to the school and asks the FBI agent to follow him. Warren is a bit puzzled, wondering how Scott knows the agent or why the FBI is suddenly interested in them, but with the school only being a few blocks away, he thinks that he will find out soon enough.
However, when the group reaches the school, they find attorney Foggy Nelson waiting for them. Apparently, Scott Summers asked him to read the professor’s will, though forgot about it later on, which is why he now excuses himself. Foggy understands that this isn’t an easy time for the troubled teenagers and offers to come back at a later time, but Scott replies that this won’t be necessary; they have to face the hard truth sooner or later. Every takes a seat, and Foggy gets right down to business and explains that he will read the will as Xavier worded it and then he’ll answer any questions that the students might have.
“In the event of my death, it is my wish that my estate be disposed of in the following manner. All of my financial assets are to be placed in a special, charitable fund – the administrator of which shall be Scott Summers!” Hearing this, Scott recalls that the professor once mentioned such a fund to him; it’s a fund to help gifted children, or more accurately, mutants like the X-Men. While Warren thinks to himself that he can’t seem to concentrate, as it is all filled with too many painful memories, Mr. Nelson continues to read the will. “My school for gifted children I bequeath to my five current students - with Scott Summers to act as trustee! And I, in turn, donate all of my personal scientific equipment to said school!” Scott admires the professor for thinking ahead, making sure that his students were provided for and could carry on even after his death.
“It is likewise my wish that all my personal belongings be turned over to my students and any of my belongings they do not wish to keep shall be donated to charity!” While Hank McCoy realizes that the professor really had no one else but his students, Jean Grey is struggling not to burst into tears. She thinks to herself that she can’t take much more of this, and fortunately she doesn’t have to, as Foggy has finished reading the will.
Getting ready to leave, the attorney says that everything will be tied up in probate for a while, and Scott answers that they understand and are sure that Foggy will handle things in the students best interest. The male students see the attorney to his car, and Scott once again thanks the lawyer after asking him to contact them as soon as the technicalities have been cleared up, Warren wishes Mr. Nelson good luck with his campaign for district attorney.
Back inside, Scott apologizes to FBI Agent Duncan for keeping him waiting, but he didn’t want to put off the reading off the will. He then asks what it is that the agents wanted to see them about, and Duncan answers hat it’s a matter of such grave importance that it may well effect the future of the entire world.
However, at the same time, an even deadlier threat is about to make his presence known. Floating in the far-flung dimensions of the Crimson Cosmos, the Juggernaut is waiting to be unleashed, when suddenly his figure is enshrouded in a blinding flash of light. It transports him back to Earth, into a laboratory of Xavier’s school. Immediately, the Juggernaut recognizes his surroundings, in fact he anticipated that his “stupid stepbrother has freed me from the Crimson Cosmos. And this time, his sentimental hopes of restoring me to his once weak relative Cain Marko - will lead to his death,” the villain declares.
Remembering the professor’s students, the Juggernaut knows that he needs to fight the X-Men before he can get to Xavier. As he keeps on gloating how he will defeat the X-Men, the Juggernaut smashes the large machine behind him that brought him back from the Crimson Cosmos – to make sure that it can not be used to banish him from Earth again.
Already wearing their costumes, the X-Men approach the laboratory. The Beast congratulates Cyclops on his expedient excuse to free them from Agent Duncan, but the X-Men’s leader answers that it was no excuse; he really felt a tremor and didn’t have the others change into their costumes for mere masquerade. Turning around the next corner, the Angel realizes that Cyclops was right. Some of the equipment did blow up and the Juggernaut is still wrecking some parts of the machine, as he too becomes aware of the mutant teenagers. Cyclops says that they knew he would eventually make a return, but he asks the Juggernaut how he accomplished to come back and why it is at a time like this.
Quite confident that he will beat the X-Men nonetheless, the Juggernaut takes the time to answer Cyclops’ questions. As for the “how,” it’s the same how he always managed to return, namely “through the stupidity of my stepbrother’s eternal hope.” Apparently, Xavier built the machine to retrieve his stepbrother from his other-dimensional prison. Cyclops understands that the professor must have built the machine secretly, explaining why he has never seen it before, and that it must have been set to activate automatically at some pre-determined time. The Juggernaut doesn’t care what Xavier’s intentions might have been, though, as all he wants is to finish his accursed stepbrother for good.
It’s only then that the X-Men realize that Cain Marko doesn’t yet know of Xavier’s recent death. When Cyclops and the Angel tell the villain the hard truth, he refuses to believe it, thinking that the mutant teenagers are lying and trying to trick him. Angered, the Juggernaut declares that the X-Men will die for this, and he hurls the Beast into a wall before the agile X-Man can dodge the attack. Even worse, Hank crashes into the auxiliary supply generator, causing it to randomly shoot bolts of sheer electricity that hits the Angel and knock him out.
Laughing at the two fallen opponents, the Juggernaut grabs another part of machinery and hurls it towards Cyclops. Even though the X-Men’s leader dodges it, he knows the machinery is now headed towards Marvel Girl, which is why he quickly turns and blasts at it with his optic beam, disintegrating the machine part in mid-air. However, that stunt leaves the Juggernaut with enough time to clog the air intake of an energizer, causing it to blow up. Cyclops tried to shield his lover from the blast with his own body, but the shock waves cause them both to black out.
When the smoke clears, the Juggernaut finds one X-Man still standing, though: Iceman. He encases the villain in a huge block of ice, but the Juggernaut says that nothing can keep him from wherever the five mutants are hiding the professor. He smashes his fists through the ice around him, but Iceman quickly replaces the damaged parts of the Juggernaut’s cold prison and tells the Juggernaut that he can continue to do so until he finally accepts that Xavier is dead. The villain refuses to believe that, however, and focusing all his anger and strength on a small part of the ice-shell around him, he managed to break it apart. A huge block of ice heads is blown directly at Iceman himself, knocking him out, just like his teammates. Almost regretting that he did not finish the young X-Man personally, the Juggernaut sets out to do what he wanted right from the start – to find and destroy Professor Xavier.
Smashing through one wall after another, the Juggernaut soon happens upon Duncan. The villain demands to know where Xavier is hiding, but the startled FBI agent gives him the same answer as the X-Men before. In turn, Duncan questions what the Juggernaut has done to the X-Men, but Cain Marko is not in the mood to answer. Instead, he grabs the agent and lifts him into the air, knocking his head into the ceiling. Reasoning that Duncan must be a friend of the X-Men, or else he wouldn’t know and ask about them, the Juggernaut declares him his enemy and tosses the agent out of a window, warning him not to interfere any further. Next, the Juggernaut goes on an exhaustive room-to-room search, but he can’t find any trace of his stepbrother. Finally, he begins to wonder if he really could be dead, and he decides to find out for sure if the X-Men were telling the truth.
A little bit later, the X-Men slowly come around. Cyclops is relieved that none of them was seriously hurt, to which the Beast jokingly replies that he has been battered so badly that even his eye-lids hurt. The Angel tells his friend not to worry too much about that though, as they’ll be the last thing he would need to use in their battle against the Juggernaut. As the winged X-Man takes to the air, Cyclops orders him to scout ahead and alert them as soon as he spots the Juggernaut.
Once again a short while later, the Angel has crossed the distance to the nearby cemetery. Just like Cyclops guessed, the Juggernaut has made his way there and now stands in front of his stepbrother’s gravestone, angered and mad that someone robbed him of his revenge. The Angel dives down and punches the Juggernaut in the gut, but he hardly feels the blow. Next, the villain tosses up some dirt and rocks at the winged X-Man, causing him to crash down.
Just as the Juggernaut moves in for the kill, he suddenly finds himself hovering in mid-air. Marvel Girl’s telekinetically holds him aloft, preventing him from reaching her teammate. Meanwhile, Iceman creates a huge block of ice for the beast to throw at the Juggernaut, now that he is distracted. Once again, though, the unstoppable foe is unharmed.
Claiming that the battle has been going on long enough now, the villain begins to emanate a strange glow and globules of sheer energy are hurled at the X-Men. Having no idea what these spheres of energy might cause, the mutants dare not let themselves be hit by them and quickly seek cover. As the Juggernaut never demonstrated this ability before, Cyclops reasons that it is a new trait he developed since they last encountered the Juggernaut. He focuses all of his optic energy in a single beam, but the blast doesn’t faze the Juggernaut. In return, even more energy pellets are erupting from the villain’s body, felling the tree behind which Cyclops was hiding.
Seeing her lover in peril, Marvel Girl tries to help. She knows that she needs to attack the Juggernaut with a mental bolt and, as she concentrates, she wishes that she would have had more time to train the use of this new telepathic power. Suddenly, the Juggernaut cries out, and holds his head in pain. He feels some sharp pain inside his brain, and he takes this as proof that Xavier must be still alive, as nobody else could hurt him this way. The Juggernaut tried to get rid of the presence in his head, but he knows that he is fighting a losing battle, when he suddenly sees the Angel lying on the ground before him. He grabs the unconscious X-Man and threatens to crush him to death if the X-Men won’t make the professor take the pressure off his brain.
Immediately, Marvel Girl stops the mental bolts and asks the Juggernaut not to harm her teammate. Cyclops explains that the professor is really dead, and that the mental power he felt originated from the young redhead and not the late professor. Jean also swears that they are telling the truth, and she points out that he must feel that the mental bolts have stopped. The Juggernaut replies that while indeed the mental attack did end, there is no way he could be sure she wouldn’t start it again, unless...
The Juggernaut doesn’t get to complete his sentence for, all of a sudden, he dematerializes and is being pulled back into the Crimson Cosmos. The X-Men wonder how that can be, with the professor dead who could have banished the Juggernaut. Cyclops replies that there’s only one possible answer; knowing his stepbrother’s evil power, Xavier must have arranged for the machine’s effects to wear off slowly if the villain wouldn’t comply.
At that point, the Angel wakes up and, to the relief of the others, he is not seriously injured. FBI Agent Duncan also arrives at the cemetery, explaining that he had a run in with the Juggernaut himself. Cyclops asks if he got hurt, but the agent says it’s nothing that a little liniment won’t cure. Next, he finally has the chance to reveal his reasons for visiting the X-Men. The incident with the Juggernaut serving as just one example, Duncan says that with the professor gone it isn’t wise for all the five mutants to be at the mansion together as they make far too easy a target for the ever growing population of evil mutants. As such, he thinks it’s mandatory that the X-Men split up and, as a beneficial side-effect, they can be much more effective if they spread themselves across the country. Escorting the five mutants back to Xavier’s school, Duncan orders the X-Men to disband and explains that they will all receive a letter from him in the next few days containing instructions where they should move to.
Back at the mansion, after Duncan has left, the X-Men ponder his words with heavy hearts. Cyclops thinks they have no choice but to obey, even though the Beast points out that the order is unquestionably unconstitutional as no body can tell an ordinary citizen where to live or what to do. Scott agrees, however he can’t deny that there was some truth to what the agent said. Spread out, the X-Men could indeed be more effective as some of them would get top the scene of some evil mutant activity much faster than they do now. He then invokes his status as deputy leader of the group and, arguing that Xavier would want them to obey Duncan, he orders his teammates to go packing, “As of this moment the X-Men no longer exist as a team!” Hesitantly, the Angel agrees, while Jean thinks to herself that she was wrong thinking that nothing could hit them as hard as Xavier’s death.
(two hours later)
Bobby Drake finishes packing his belongings and he realizes that he can’t put off leaving any longer. He says to himself that it feels like he is being orphaned. As Jean walks down the stairs from the level containing the living quarters to the main entrance hall, she thinks that not only she is losing the family she has known for the past years but also possibly the man she loves. All five students meet for the last time and bid each other farewell. Then they silently leave the building, all of them walking off to their cars or the cabs waiting for them.
Standing in the doorway, Scott asks himself if he is actually going to stand there and let the only girl he would ever love walk out of his life. Jean is lost in similar thoughts, against her hopes Scott isn’t coming after her, and she wonders if this means he doesn’t care for her after all. And, if they are going to be sent to different parts of the United States, she might never find out for sure.
An angry mob has surrounded Bobby Drake and Cyclops, and one of them says that it looks like their powers gave out. Several rifles pointed at them, Cyclops raises his hands, and thinks to himself that the man guessed it – he has overused his optic beam, and he fears what the angry townsfolk might do to them now. Seeing his neighbors like this, Bobby says that he has been a fool for thinking that he would be given a fair trial. As far as he is concerned, the people are no longer acting like human beings but more like a wild pack of animals. One of the men tells Bobby to save his breath for later, as he’ll need it when they string him up. Yet another attacker already has some rope in his hands and calls out to his friends, “C’mon, boys! Let’s stretch their necks!”
The sheriff interrupts, saying that there’ll be no lynchings in his town, and that he’ll make sure that things are handled by due process of law. Anyone thinking otherwise will have to go over him. The sheriff orders the angry men to put the guns down and to go home, as he can take the two mutants to jail by himself, but Cyclops knows that the mob is too angry to listen to his words.
As the sheriff pushes away a gun that’s pointed at him, some of the angry men declare him a mutant-lover, and decide to hang the two mutants no matter what he says. While some of them hold the sheriff back, the others begin to tie up Scott and Bobby, not listening to the sheriff’s protests nor his threats that he will make sure that they all will be put to jail for this.
Next the two mutants are being dragged through the streets. Cyclops says that they meant no harm, but Bobby replies that it’s no use; they will never listen and his ice powers are too weak to snap out of the ropes. Cyclops whispers to him that his power is too drained as well, and that he is putting up a front so that the angry townsfolk won’t suspect that he is stalling for time. He recommends that Bobby does the same, and so the two young mutants led themselves be dragged through the streets of the small town, until they are led to a tree. As some of the men throw a rope over one of the thick branches, Scott feels that he will only need a few more seconds. Bobby though, doesn’t believe in miracles.
Maybe he would, if he knew Scott’s mentor, Professor Charles Xavier. About two miles away, the professor is steering his car towards the small town, praying that he is not too late. He mentally contacts Scott and immediately gets a grasp on the situation. He then orders Scott to break free and head for Drake’s home. Receiving the telepathic message, Scott knows that help is on the way. He does as told, and he finds that his optic beam has returned, allowing him to blast at the nose that one of the men was just about to wrap around Bobby’s neck. In panic and fear, some of the men run away, and Cyclops tells Bobby to head for his home and to use his powers along the way, if they are working again.
Not too far away, one of the men aims his rifle at Scott and is about to pull the trigger, but Bobby spots him in time and stops him by throwing a few ice-balls in his face. Cyclops kicks another attacker in the head and punches another one’s face, allowing the two mutants to run off, even as some other men are shooting at them. Scott tells Bobby to run for his life, and the young mutant does, even though he has no idea what good it will bring them, as the angry townsfolk can come after them.
Indeed they do and, as soon as the angry men realize that the two mutants are headed to the Drakes’ house, they take a short-cut to the house. Hiding in an alley, Cyclops and Bobby are relieved when they see the men running off in another direction. Bobby points out that he knows an even shorter route to his place, and the two mutants try to make it there before the men do.
Along the way, though, Scott receives another telepathic message not to worry anymore, as Xavier has already telepathically handled the mob and everything is under control. Once they reach the Drake’s house, Xavier introduces himself to Bobby and explains to him and the boy’s parents that he erased everything that happened from the townsfolk’s memories. The professor then says that the important thing is what will become of Bobby, and he already has a solution at hand, as his parents have consented for him to become a student at Xavier’s school. The bald man explains that there he will receive training in the use of his mutant powers, so that he can use them to combat evil mutants. Additionally, at the school he will be safe from similar attacks like the one that occurred today.
Bobby agrees to come along, but worries about his parents. Xavier replies that he will alter their memories as well; while they will know that he is a student at his school, they won’t recall his being a mutant. Bobby is convinced, and he hugs his mother as he says his goodbyes. Talking to Scott, Xavier states, “today we say goodbye to the X-Man - and begin the era of the X-Men!”