The five X-Men are in the main chamber of Factor Three's hollowed-out mountain fortress, the grim visage of the Mutant-Master on the huge video-screen mocking them. He says that it doesn‘t matter that they escaped the fate he had sentenced them to, for they are unable to prevent Factor Three's forces from bringing about World War Three, in which the inferior race of Homo sapiens will perish. As the giant image fades, the five mutant teenagers are left wondering. Cyclops finds it strange that the Mutant-Master seemed unworried, although they are free to try and stop him, and Jean agrees that it was almost as if he knew they could never find him in time or rescue the Professor and the Banshee.
Suddenly, the Beast chimes in, saying that the Mutant-Master might be correct. That is, if they don't abandon the base immediately as it is about to blow up. Angel asks how his teammate could know that, but Cyclops tells him to save it for later and orders the X-Men to leave as soon as possible. Fortunately the mutants happen upon two Magno-Disks, the strange aircrafts that Factor Three have been using, and find them rather easy to pilot.
Once they are hovering above the mountain-base, it still being intact, Iceman and Cyclops question the Beast on his hunch about the base blowing up. Hank points down to his feet, explaining that the extra-sensitive sensors in his toes detected the presence of a ticking bomb underneath the floor. Hearing this, Iceman belittles his friend; they had to run like rabbits just because of his itching toes?
Right then the mountain blows up, almost knocking the two Magno-Disks out of the sky. A bit embarrassed, Bobby asks whether they could strike his last remark from the record, but Scott reminds him that they have more important things to do than keeping score – like preventing Factor Three’s mad scheme to set off World War Three. However, as they don’t know where exactly they will strike, Cyclops decides that they can only wait until the Mutant-Master tips his hand. Therefore, he sets a course back home, to the school.
Meanwhile, in another secret headquarter of Factor Three, the Mutant-Master and the Changeling have followed the X-Men’s every move. The Mutant-Master curses at the five mutants for escaping yet again, but it won’t alter anything. He says that his plan to set East against West must still carried out on schedule by the evil mutants. The Changeling confirms his superior’s order, though he also points out that there’s something he doesn’t comprehend: How did the Magno-Disks come to be left completely operational in the other base?
The Mutant-Master calls the Changeling a fool for wasting thoughts on such insignificant matters. When the Changeling protests at being called a fool and points out that, immobile as he is in his hovering platform, the Mutant-Master depends on his help. For example, it was he who recruited all the evil mutants. Hearing this, the Mutant-Master has an outbreak of bad temper. He puts the Changeling back in his place by threatening to dispose of him with one of his many lethal weapons. He even backs up his threat by firing a deadly laser right next to his second-in-command that could have easily obliterated him.
The Mutant-Master laughs at the Changeling, saying that he doesn’t need any mind-reading powers to sense his lackey’s great fear. The Mutant-Master tells the Changeling to remember that, while he might be a fellow mutant with a power that someday might prove useful, he is in no way the equal of the undisputed leader of Factor Three.
Never before has the Changeling seen his master that way and, frightened to the bone, he quickly swears that he didn’t mean to challenge the Mutant-Master. He only wants to serve their common cause and destroy the race of the Homo sapiens. Next, the Mutant-Master once more retaliates his plan to take over the world – turning the eastern and the western countries against each other will result in a nuclear World War, a war that will end the civilization of Homo sapiens, with mutants inheriting the Earth. And all this is only possible because of the Mutant-Master’s many weapons and devices, such as the new base, a mammoth floating sphere undetected by even the most modern radar, from where he and the Changeling can watch the events unfold. Even now, the Mutant-Master says, are the Blob and the Vanisher putting his plan into operation, while Mastermind and Unus are standing by, awaiting further orders.
Once more the Mutant-Master tells the Changeling not to speak of such unimportant details like the X-Men escaping the Oblivio-Ray. If they dare to interfere again, he could easily destroy them with his weapons such as the sonic shock-wave ray. That said, he activates the device, letting the Changeling feel its effects first hands. His head being filled with deafening thunder, the Changeling begs for his master to turn off the weapon, swearing absolute loyalty.
Still hovering above his second-in-command, the Mutant-Master orders for the Changeling to contact the Blob and the Vanisher behind the Iron Curtain to ascertain that all goes well. The Changeling expresses concern, bringing up the possibility of someone intercepting the message, but when the Mutant-Master angrily asks if he dares question his will again, the underling quickly falls silent.
Carrying out the Mutant-Master’s orders, the Changeling uses a huge radio generator to contact the Blob, only to learn that everything has gone according to plan. Reporting this to the Mutant-Master, the Changeling is told to leave the chamber. All alone, the Changeling thinks about his master’s arrogance growing more intolerable with each minute. He wonders whether he and the other evil mutants have exchanged their roles as feared outcasts from humanity for those of slaves, but he decides to ponder that question later, after the world of Homo sapiens lies in radioactive ruins.
Likewise, the Mutant-Master makes up his mind on his second-in-command. He considers the Changeling to be restive and resentful, though he is sure that he doesn’t suspect anything about the Mutant-Master’s true agenda. And, even if he would, the Mutant-Master is positive that it wouldn’t matter any more. Neither he nor all the evil mutants alive could stand again someone of his power. When the mutants rule the planet, it will be the Mutant-Master who rules the mutants.
At the same time, at Xavier’s school for Gifted Youngsters, the X-Men consider themselves fortunate almost beyond belief. Somehow, Cerebro has managed to pick up the two sets of radio signals that the Changeling sent to the other agents of Factor Three, and they now know exactly where the villains plan to strike. The mutant teenagers agree on their top priority being to prevent the nuclear holocaust, whereas finding the Mutant-Master or rescuing Xavier and Banshee are secondary goals they hope to accomplish.
They quickly depart to the two locations in their borrowed Magno-Disks, their only hope of reaching the villains in time. Saddened by the fact that the group has to split up, Hank and Warren attempts to cheer Jean up, as she looks out of the craft’s window, seeing the other Magno-Disk with Scott and Bobby inside fading out of sight. She worries that she might never see the one she loves again, but immediately reprimands herself to even consider the possibility of the X-Men failing.
(an incredibly short time later)
Marvel Girl, Beast and Angel have landed their craft in the woods near a certain location in Eastern Europe. The Magno-Disk flew so fast that no existing radar could have detected them. Angel performs a quick reconnaissance flight, during which he spots a medieval castle nearby being guarded like Fort Knox. Inside, there’s the top-secret meeting of every important military leader from the East taking place, the meeting that Factor Three want to sabotage with a bomb they have planted somewhere in the castle. The X-Men know that, if anything were to happen to these men, it would sure look like an American plot, so they set out to find the explosives before its too late.
While the Beast climbs up the outer wall of the castle, Angel carries Marvel Girl up to the top. Unfortunately, they are spotted by a guard and, although the Beast eventually disarms him, he can still manage to fire one shot that is heard by the other troops. Immediately, the entire castle is alert and Hank finds himself facing an entire battalion of troops. But, landing blow after blow, the beast takes out several of the soldiers and keeps the upper hand.
Having safely landed in another level of the castle, Jean wonders how long the Beast can last against the troops and whether they should help him, but Warren reminds her that it was the plan for the Beast to serve as a distraction, so that they could carry out their mission. Trying to get to the meeting of the military leaders, the two X-Men enter a hallway, only to run straight into the Blob, the Vanisher and a handful of hooded Factor Three operatives.
Inside Factor Three’s flying sphere, the Changeling is checking up on the prisoners, showing the still immobilized Xavier and image of the supposed atomic Armageddon on a device called Predicto-Scope. The professor calls his captor mad, entirely convinced that his X-Men will find a way to stop Factor Three’s plan. The Changeling finds Xavier’s faith almost touching, however he tells him that the Factor Three agents have been warned about the X-Men’s presence and will be waiting for them. The mutant teenagers will die even before the human race goes down in the nuclear holocaust.
Speaking of which, Xavier asks, if the entire planet becomes a nuclear wasteland, wouldn’t the mutants be doomed to die too? The Changeling knows an answer to that question though; with his scientific expertise, the Mutant-Master has devices ensuring their survival. He goes on that Banshee and Xavier were only allowed to live so that they could witness Factor Three’s ultimate triumph.
Xavier calls Changeling a fool and warns him that the Mutant-Master means to betray him as soon as the humans are destroyed. Not willing to hear any of that, the Changeling slaps his helpless prisoner in the face, and orders him to be silent or else he will be executed at once. Just having entered the room on his hovering platform, the Mutant-Master interrupts him, saying that the Changeling will execute no one. It’s only for himself to decide who lives and who dies.
The Changeling apologizes for overstepping his authorities, and begs for his master not to use any of his deadly weapons again. This time, the Mutant-Master is more forgiving, as he states that ambition is a quality he detests in those who serve him. Then, he orders the Changeling to leave the room, as he wants to work in the chamber undisturbed.
By now, Cyclops and Iceman have reached the American ICBM base, from where Factor Three wants to launch the missiles against the East. Having listened to the X-Men’s story, the high ranking officer in charge of the base doesn’t believe a word – he thinks it absurd and impossible that someone could infiltrate his base, and he orders the two costumed mutants to leave within ten seconds. Cyclops apologizes to the colonel, saying that he isn’t leaving them much of a choice, and threatens that they would destroy all the base’s missiles if the military won’t investigate their story. Of course it’s a bluff, the base actually containing too many missiles for the two X-Men to dismantle.
The colonel thinks he has heard enough and orders the guards to lock up the two mutants, which is easier said than done. Iceman freezes up the soldiers' hands, so that they can’t shoot, and Cyclops blasts a hole into the building’s wall, allowing them to get out real fast. Outside, they are met by more soldiers and easily dispose of them, but the two X-Men know it’s only a matter of time before somebody gets hurt.
Still trying to give the mutants a chance to surrender, the soldiers are firing rather low, which Cyclops sees as an opening to cross the ground towards the missile bunkers. Once there, he and Iceman start destroying as many missiles as they can, well aware that they might run out of powers soon. But, for the sake of the world, they know they have to destroy all the missiles... or die trying.
A continent away, the remaining X-Men feel just the same, facing overwhelming odds. Not wanting to get his own hands dirty, the Vanisher orders the hooded Factor Three agents to destroy Angel and Marvel Girl with their ray-blasts, and Warren is too far away from them to reach and disarm them in time. Fortunately, Jean buys him a few precious second by levitating a nearby table into the line of fire, shielding Warren long enough to fly above them. He plans to get past them all, so that he can make his way to the meeting room and warn the military leaders from the East about the danger they are in. However, the immovable Blob gets in his path, obviously teleported there by the Vanisher. Marvel Girl tries to help, smashing some debris on the Blob’s head, but it only gets the Blob annoyed.
Angel turns to the hooded agents again and disarms them easily. However, the ray gun’s being too complicated for him to use at a second’s glance, Warren decides to toss them out of the window, where they won’t do any harm. As the battle continues, he wonders what’s keeping the beast, as he should have caught up by now. Jean, meanwhile, faces problems of her own, busy dodging the Blob’s punches by levitating herself out of harm’s way. But the experience is tiring her, and she knows they are running out of time.
The Angel shares her concern, when he suddenly hears the Vanisher’s voice behind him, telling him not to move and threatening to gas him with his weapon. Warren doesn’t obey, though, he swings around and quickly flaps his wings, sending the gas back at the Vanisher himself. Marvel Girl also makes use of the unexpected turn of events, her telekinetically concentrating enough of the gas around the Blob’s head so that he passes out. The Vanisher is still conscious, though, and to prevent him escaping, Jean tries to telekinetically spin him around to make him dizzy. It doesn’t work, though, and he teleports away, leaving the Blob behind.
Warren tells her not to take it too hard, for they have to warn the general now, when suddenly the hooded Factor Three agents blow up, them having been androids all along. The blasts are relatively small and controlled, but enough to briefly floor the two X-Men. When they come around, they are already surrounded by numerous soldiers, pointing their guns at them and accusing them of trying to assassin their leaders.
Marvel Girl is surprised, but Warren explains that it makes sense, for all the military knows they are the only ones present along the unconscious Blob. Still, he tries to reason with the guards and asks them to alert their leaders of the terrible danger. It’s no use, though, and the two X-Men are led to a dungeon, where they are also reunited with the Beast, who had been captured earlier. Hank, being unable to break the bars with his strength, and them sharing a prison cell with the unconscious Blob, who could wake up any time, the situation is dire for the three X-Men.
Thousands of miles away, the Mutant-Master sits in his base’s vast communication complex, where he has followed the X-Men’s every move. Except for the capture of the Blob, he exclaims, everything is going according to schedule. In few minutes, an explosion will occur behind the Iron Curtain, and a brace of missiles will lift off from the United States. And, in that final moment, he will have achieved victory!
Behind triple-locked steel doors... in a forbidding, seldom-visited section of Professor Xavier's School for Gifted Youngsters... stands row upon row of cold, silent file cabinets... Yet, if they could speak, they would unveil a treasure-trove of little-known information on countless subjects... from the trivial to the unimaginably vital... And, one of these myriad metal drawers... identified only by an innocuous typewritten card... hides the most carefully-guarded secret of all... the secret history of the mysterious beings known as... the X-Men!!
Somewhere in a heavily guarded building in Washington, the capital of the United States, two suited men are watching an urgent news bulletin that has just interrupted the regular TV program. The bulletin shows some sort of a riot, several men angrily yelling and raising their fists up in the air. A reporter explains that what the audience sees is the reaction of the crowd to the discovery that one among them was super-powered mutant. Luckily for him, or perhaps for them, the mutant fled rather than face the crowd's wrath. The reporter goes on that scenes like this are happening all over the county...
Fred Duncan, one of the two men has seen enough, and asks his colleague Bill to turn off the TV. He is now even more convinced that they have to act, that they have to begin an investigation of this so-called “mutant menace.” Bill replies that its Fred's decision, but he would like to suggest they let the press in on it, as many cities are already reporting conditions of near panic. Thus it is that a fateful chain of events is begun, one which is to have the gravest implications for mankind.
(the next morning)
Passing by the main entrance of a certain mansion in New York's Westchester County, a delivery boy flips the newspaper near the door and thinks to himself how this place always gives him the creeps. Although the house is on his route for a few months now, he has never seen a sign of life, other than that somebody has left him the collection money under the doormat once in a week. Yet, no sooner has the uneasy boy departed, the door opens and a hand reaches for the newspaper on the ground. It's the hand of the mansion's owner and apparently sole occupant - Professor Charles Francis Xavier.
Spotting the bold headline on the papers' front page – “MUTANTS” - Xavier thinks to himself that finally the very thing he knew always would happen one day has come. Quickly reading through the entire article, Xavier learns that the human race has discovered the presence of mutants in their midst, and that the FBI is beginning a special investigation as of today. To Xavier, this means he cannot dare play the role of recluse any longer and that he must leave for Washington at once. Well aware that both humanity and those it calls mutants must be protected, Xavier hopes that he has not delayed too long. Ever since the tragedy that befell his stepbrother in Korea, Xavier has been living a life apart, isolating himself from everyone else, trying to blot out all memory of that event, but now he knows that the mansion has not only been a refuge, but also a prison.
He moves his wheelchair to a specially designed elevator, taking him into a hangar bay underneath the house. Soon, Xavier is already airborne and passing the Potomac River, while traveling to Washington in a high-speed helicopter. During the flight, Xavier recalls how he had told himself for months that he would never again involve himself in the affairs of Homo sapiens. The irony that it took merely one newspaper article to change his opinion doesn't escape him, though.
As he attempts to enter the FBI building mentioned in the newspaper article, Xavier is met by three guards. They stop the professor, saying that nobody is allowed in unless they have been sent for. Xavier politely answers that he appreciates the guards' concern for their superiors' safety, but the fact remains that he goes in. While the guards make fun of the man in the wheelchair, he suddenly uses his mental powers on them without warning, forcing them not only to let him pass, but also to forget about the entire incident. Xavier thinks it better that way, he doesn't want anyone to know of his powers unless it's needed.
Inside the building, the scene repeats itself several times, and Xavier makes his way safely through a number of hallways and offices. None of the FBI personnel remembers the man in the wheelchair, as he continues to search for the man who is conducting the mutant investigation.
Meanwhile, on another floor, Fred Duncan and Bill are watching a short film that has been recorded by chance by a TV news camera, right before the riot the other day. In fact, they are already reviewing it for the tenth time and Bill asks what more Fred thinks they could learn from it, to which the superior agent says he doesn't know. Still, this film is their first real clue, the only proof that mutants even exist, so there has to be something in it.
The film start with a huge crate containing an air-condition unit being lifted atop a midtown office building. Suddenly a beam of scarlet light hits the crane, breaking it. The seemingly doomed spectators below all run away in panic except one, a teenager wearing an odd pair of red glasses. Fred and Bill look on, as the young man reaches for his temples, grasping the sunglasses, and in the next instant red light burst from his eyes, disintegrating the huge crate into thin air. However, within a matter of seconds, the crowd begins to turn on their unknown benefactor, shouting out loud that a man possessing such abilities is a monster and by far more dangerous than a falling crate. Some of the men raise their fists in anger, and plan to do something about the mutant in their midst, who fortunately has managed to slip away in the confusion.
The short film at an end, Fred Duncan sums up the humans' reaction - apparently there's something about the thought of mutants, of otherwise normal human being born with some extra power that drives mankind to distrust, fear and even hatred. Duncan suspects that it was the same youngster who saved the crowd whose power had endangered it - probably accidentally; but Bill replies that they can't be sure about that. Fred Duncan agrees; for that they need to confront the mutant himself.
“When and if you do confront that lad, gentlemen, may I suggest that I be there! My presence may be more important than you dream! My name is Xavier, Professor Charles Xavier,” the telepath answers, making his presence known to the two FBI agents. Fred and Bill are startled at the sudden appearance of the man in the wheelchair, wondering how he could have gotten in there. Where Bill is concerned, the “how” doesn't matter so much, as he sure knows how to get the intruder out again. Thinking he has nothing to fear from an invalid, Bill pushes the wheelchair as hard as he can, but it doesn't move. Xavier calmly explains that this is his doing, that the agent only thinks he is pushing with all his might.
Deducing that Xavier must be a mutant then, set on stopping the investigations, Fred Duncan draws his gun. The professor tries to explain that while he is a mutant, his purpose is far different than he suspects, but the FBI agent is not convinced. Although Xavier has made no overt move yet, Duncan decides to fire a few warning shots at the wall, if only to alert the guards, but he finds himself unable to pull the trigger. Apologizing for this somewhat melodramatic use of his vast abilities, Xavier asks the two agents to listen to him for a few moments, to let him explain who he is and why he sought them out.
Xavier then introduces himself once more and, after describing his own powers, he explains that, as the two agents may have already suspected, there are good mutants and evil ones. The teenager they saw in the short film is doubtless as frightened of the crowd as they of him, the professor adds. Next, Xavier proposes his idea – he suggest helping the FBI and the human race by tracking down the mutants in the United States himself; reasoning they might scarcely trust an outsides, but perhaps one of their kind.
Duncan admits that he is making sense, and also that while they have a few leads on who some of the mutants are, the FBI has not yet figured out how to approach them. Xavier argues that, if they are hounded or persecuted, the mutants might band together and become the very menace that are feared to be. Duncan agrees and decides to give it a try. While they will supply Xavier with the info they have, in return they expect the professor to report at regular intervals about his progress. As they shake hands, Xavier says that he hopes they have reasoned correctly, for the survival of all humanity may depend on them.