Sitting on his huge hovering platform, the Mutant-Master watches the events unfold on two huge view-screens in front of him. One displays Cyclops and Iceman taking on an entire missile base somewhere in the south-western United States, the other monitor shows Angel, Beast and Marvel Girl trapped in the a prison cell together with the Blob somewhere behind the Iron Curtain. Laughing at his enemies' efforts, the Mutant-Master is confident that his plans will succeed.
At the missile base, Cyclops and Iceman are having a hard time outrunning the fire of some strafing planes, until Scott orders Bobby to cover them with an ice igloo. The younger X-Man does as told, although he says it wouldn't do much good against the military's high-caliber bullets. However, a couple of seconds later, with the planes flying by without firing at them, he understands what his leader's plan was - the sun's glare of the ice blinded the pilots, thus they were unable to shoot at them. The incident buys the two X-Men the needed time to cross the distance towards the building they were headed for.
Inside the structure, the two X-Men are met by a soldier, but Iceman traps him in a block of ice before he can fire his gun. The other guards receiving the same treatment, the two X-Men make it to the base’s air-filtration system in no time and Iceman covers it with a think layer of ice to make sure that Factor Three’s plan to pump a narcotic gas in it won’t work. However, Cyclops reminds his comrade to stay alert, for there sure must be some Factor Three agents nearby, who were to fire the missiles once the military was asleep. Bobby, however, is convinced that they must have returned to the Mutant-Master by now.
As if to prove him wrong, suddenly two giant tentacles emerge from the machines around the two X-Men, pinning them against a wall. Cyclops notes how they can’t be harmed by their powers, as if they were specifically designed to capture them. Whatever Iceman and Cyclops try, the tentacles won’t break and Scott wonders out loud what material they could be made of.
A person entering the room answers that it is of no consequence to him anymore, as within moments he will be dead. Cyclops turns his head to the door and sees Mastermind and two of Factor Three's hooded androids enter the room. Somewhat impressed, Scott asks how they managed to get past the military troops that chased the two X-Men, to which Mastermind answers that it was quite easy, due to his power to cast illusions.
Hearing this, both Iceman and Cyclops suspect that the tentacles holding them are mental images of Mastermind too and, concentrating really hard, they see through the deception. Free again, they barely have time to catch their breaths, for Mastermind didn't come without back-up. Unus lunges forward, Cyclops' optic beam bouncing off the forcefield surrounding the untouchable mutant.
Half a world away, the other three X-Men find themselves in a well-guarded prison cell. Beast mentions that the door is too thick; his strength won't get them out. However, Jean finds that she has rested enough to use her telekinetic powers again and she lifted a dozing guard from his chair, towards the door. Hank reaches through the bars and grabs the guard from behind, providing Jean with enough time to telekinetically grab the keys and unlock the door. As they escape, the three X-Men know that they have to hurry if they want to stop the bomb from going off.
In some other room of the castle, the eastern military leaders confer, still unaware of the grave danger they are in. They even ponder declaring war on the United States because of the X-Men, whom they believe were sent to assassinate them. Right then, the Beast interrupts and tries to convince the military leaders that this was not their intent, but of course they don't believe him. Immediately, some soldiers try to subdue the Beast, but Angel comes to aid him, knocking out some of the attackers from above. Marvel Girl also arrives and, having telekinetically probed the room, she discovers the bomb to be in a certain briefcase. She lifts it up in the air, trying to get it out of harms reach.
All of a sudden, the Blob too enters the fray. Obviously, he awoke sooner than the trio of X-Men expected and followed them throughout the castle. He lands a punch at the Beast and declares that the X-Men won't be able to thwart Factor Three's plan, because there's just one minute left before the bomb blows up. Beast tries to repay the Blob in kind, only hurting his hand in the process, because the massive mutant willed himself to be immovable. Next, he grabs the floating briefcase before Jean can react telekinetically.
In the military base in the United States, Iceman and Cyclops aren't doing much better. Unus lands blow after blow on Cyclops, whose optic beams are of little use, whereas Iceman finds his aim being messed up by Mastermind wrapping illusionary bands around his arms. The villains gloat that they have already won, when Cyclops tells his teammate to form some ice before him. He blasts at it with his optic beam, creating a fog-like icy mist, making it hard for everyone to see.
Mastermind and Unus decide to better make their escape now, before the military troops breaks in. No sooner have they left then the soldiers indeed enter the chamber. They too are thrown off-guard by the thick wintry fog, but it soon clears and they soldiers find the X-Men gone. At least, one of the generals says, they couldn't fulfill whatever traitorous mission they had in mind.
Already departing in the borrowed magno-disk, Scott and Bobby congratulate each other as they have truly accomplished what they came for - they thwarted Factor Three's plan to release a narcotic gas through the air filtration system and take over the base.
In Eastern Europe, Hank warns the Blob off the deadly explosives in the briefcase he's holding, but the villain says that his massive body could withstand the blast, only everyone else present would be affected. As Marvel Girl is unable to telekinetically wrench the satchel from the Blob, she comes up with a different approach. She argues that the mutant-master surely wouldn't take a chance on the Blob's capture and others learning of his plan, so the bomb must be strong enough to kill even him. The Blob responds that she must lie, then again, he also thinks that she might have a point and that there's no use in taking chances. Intending to watch the explosion from a safe distance, he drops the briefcase and escapes through the castle's outer walls.
The briefcase beginning to vibrate shows the three X-Men that the bomb is about to explode in the matter of seconds. Angel takes it into his hands, flies up into the skies and hurls it away as fast as he can. The detonation occurs in free-fall, nobody within range to be harmed by it. The eastern military leaders now realize that the X-Men spoke the truth – there was really an assassination attempt on them. Still, it could be the case that they were sent to spy on the generals. While they still argue whether to imprison the trio of X-Men or not, Angel picks up his two colleagues and flies off with them, to the nearby magno-disk.
Meanwhile, the Mutant Master has landed Factor Three's large spheroid base somewhere in the mid-western United States, and contemplates the recent events. He didn't think it possible that the X-Men would thwart his plans, and partially blames himself for he let them deliberately escape, so that they would receive the blame if his scheme was thwarted. As he continues his ramblings, he suddenly notes that his second in command, the Changeling, is not in his usual place. However, he decides it doesn't matter any more, for the Changeling would only try to stop him if he guessed his true intentions. Suddenly, the Mutant Master senses someone approaching, and readies himself.
A few minutes later, Cyclops and Iceman enter the structure, their magno-disk's sensory devices having led them to the base. Scott advises his younger teammate to proceed with caution and, right on cue, a defense mechanism starts blasting at them. Both Scott and Bobby leap out of harms way, only to find the Mutant Master on his platform hovering before them. He declares that they won't leave the base alive and, when Cyclops fires an optic beam, it becomes clear that the entire platform is protected by a force-field.
Before the two X-Men can start a new attack, someone else enters the room, saying that they will handle these "runts." It's the four archenemies of the X-Men - Vanisher, Blob, Unus and Mastermind. Scott and Bobby thinks themselves outnumbered, but the timely arrival of the other half of the X-Men proves them wrong. A battle is about to start, and Cyclops already barks orders to the rest of the X-Men, when suddenly a voice interrupts, telling everyone to stop, as there's no need for mutant to battle against mutant. It's the voice of Professor Xavier.
Xavier explains that he has escaped to warn the four villains against their real enemy - the Mutant Master. Hearing his name, the Mutant master laughs at the telepath, asking if he really expects his followers to take the word of their sworn foe over that of their leader, all just to save the weakling race of Homo sapiens. Unimpressed, the professor repeats his accusation and dares the Mutant Master to explain why he leads the so-called evil mutants in their unholy crusade against humanity. The villain gives the standard answer of mutants being Homo superior and as such destined to rule the planet, but Xavier calls him a liar and says he has evidence to prove it. He demands an answer for why he didn't sentence the X-Men to death when he had the chance, rather than to the oblivio-ray. Next, Xavier brings up the two magno-disks left carelessly in the old base, which enabled the five mutants to escape from its explosion. It's as if he wanted the X-Men to get out alive.
As the villains begin to believe the Professor's words, the Mutant Master becomes outraged and orders them to kill Xavier immediately. This, however, is only get another evidence, as Xavier points out that this can only mean that he doesn't want the four villains to hear what else he might have - namely that he figured out the real reason he wanted to start a world war was to not to rule the planet, but to destroy it. Repeating that he did everything in the name of mutant superiority, the Mutant Master knows that he is fighting a lost cause, and he can't hide the deadly truth much longer. He presses a switch that increases the platform's forcefield and, deciding that the villains have outlived their usefulness, he orders his androids to kill everyone present. A fight starts, with both the X-Men and the four evil mutants doing quite well against the overwhelming number of androids.
In a neighboring chamber, Banshee comes around. He has a major headache, and barely remembers someone releasing Xavier and him from the stasis tubes, only to quickly knock him out. He follows the sounds from the fight and opens the door to the next room. He barely has the time to wonder about the X-Men and the evil mutants side by side, as he is spotted by one of the androids and aims his ray-blaster at him. Banshee defends himself with a sonic scream and hits the right sonic frequency, the android being shattered by it. Knowing that this shriek won't hurt humans or mutants, he raises the pitch of his cry, hoping to deactivate all machinery in the room. What happens next, nobody was prepared for.
The Mutant-Master's platform breaks apart, but also his helmet, his face and his fake body that was sitting behind the desk on top of the platform. As the debris falls down to the ground, a huge green, tentacled alien is revealed, which was residing inside the platform. Banshee is still using his sonic scream, which the alien doesn't like one bit. Stating that it comes from the star-sun Sirius, it orders the Banshee to bow to his will and stop the noise. Unus starts hitting the alien as well, letting out his frustrations that he was deceived by the "mutant master." Noticing the effect it has on the alien, Banshee can't resist to shriek one octave higher, placing the "mutant master" in great agony. With one of its tentacles, it reaches for a fatal button, causing all of the androids to explode.
Suddenly, a second Professor Xavier wheels into the room, and the surprised X-Men wonder which of them is their real mentor. The matters is quickly solved though, as the newly arrived one can confirm his true identity by using his telepathic powers, whereas the first one was only using Xavier's voice. Marvel Girl grabs him telekinetically, and correctly guesses that he must be the Changeling in disguise. Wondering why the Mutant Master's right hand man would impersonate him, Xavier looks over to the huge alien figure and witnesses its final moments.
"Defeated - disgraced! There was no way out - no way but death! I came from Sirius - to conquer a world - but I failed... But, the final blast did its work! My brain feels heavy - tired - a Sirian my know destruction - but never capture -" Even as he speaks, the alien body withers away before the assembled mutants eyes. Finally, after what Marvel Girl calls the first interplanetary suicide, there are a few tense seconds of silence.
Then the somber mood is broken, and the X-Men wonder what to do with the Changeling and the four evil mutants, who are ready to fight for their freedom. However, Xavier tells his students that they fought side by side with them, so they should also part as allies. Unus says that, when they meet next, it will be as enemies once more, before revealing that he set the entire base to self-destruct.
Soon afterwards, four magno-disks streak into the sky, two of them carrying Xavier, Banshee and the X-Men. Cyclops and the professor discuss Factor Three incident, both agreeing that the four villains should have been able to see through the Mutant Master's plans too, if they were not so blinded by their hatred towards baseline humans. Still, Xavier says that no matter what happens next, they can always remember the day when there were no "good" or "evil" mutants, but a handful of men protecting the planet from a common foe. And that is something he draws hope from.
The magna-disks have just enough fuel to take the team home and, once they enter the mansion, Jean gets rather excited as she remembers a pet project of hers, which she started with the professor's permission shortly before the X-Men's battle with the Juggernaut. She hands each of her teammates a package, saying that they'll find new costumes in them. Bobby complains that it'll be just the same old uniforms with some trimming, and mocks Jean by asking if she added blue belts this time. However, she tells him and the others to try them on and see for themselves.
When they meet again a few minutes later, the male X-Men realize that they have received different, individual costumes. Warren says he feels like he looks like a true angel now, and even Iceman - who basically has no need of a costume at all - received new boots and gloves.
However, they want to know why the got this new costumes, and Banshee admits that he is curious about that a bit too. Xavier happily says that the answer is simple - it was long overdue. He considers the X-Men scarcely children anymore, as they have proved themselves a hundred times in combat. He thought it was time they looked like individuals and not products of an assembly line.
Noting that Hank is not smiling like the others, Jean asks him what the matter is, and he admits that it might take him a while to adjust to the tight sleeves of his costume. Angel responds that he should cheer up. After all, Jean could have helped him to live up to his nickname by knitting a fur outfit with a cute curly tail.
In the streets of a sprawling city, an amazed crowd has made a shocking discovery - among them is a mutant. A construction worker is the first to yell the accusing word at the teenager wearing a pair of oddly colored sunglasses. Some other man agrees; the teen has to be a mutant. How else could he have destroyed the falling air-conditioning unit just by looking at it?
The young man thinks to himself that a stray optic blast of his caused the unit to fall, leaving him no other choice but to obliterate it. However, in saving the crowd, he has revealed himself and he notices that the crowd is turning into an angry mob right before his eyes. He runs away as fast as he can, fearing for his very life. Luckily for him, he is able to hide behind a nearby corner, with the angry men chasing further down the street they saw him enter.
As they run by his hiding spot, the young man overhears the men talking about his "death-ray," and how they how they can "handle him" once they catch him. However, they are only one of his problems; the unfortunate mutant also knows that a TV camera got a shot of him, so he dares not going back to the orphanage where he lives. Fearing that he will be tracked down sooner or later, he decides to leave the city. He makes his way to some railway tracks and hops aboard a freight train just starting to roll.
In Washington, FBI agent Fred Duncan hands Professor Charles Xavier the information the FBI have gathered on probable mutants in the United States. He admits it’s not much, but it’s all they have got right now, and Xavier says it will have to do. One description on the brief list arouses the professor's interest - a boy named Scott Summers. Duncan remembers him to be a case with strange eyes, an optometrist having confidentially alerted the FBI.
Before leaving, Duncan decides to call first to make sure that Summers still resides at the Sunset Orphanage that is mentioned in the file. The person on the phone is quite surprised to be talking to the FBI, but they mention that Scott Summers went to New York with their supervisor, Mr. Lamb, this morning, and somehow disappeared. The police are already searching for him. Having eavesdropped telepathically on the conversation, Xavier decides its best that he pays the optometrist a visit while Duncan and his men organize a search for the boy.
Not much later, Xavier finds himself in another part of town, in the optometrist's practice. The professor urges the doctor to tell him everything he knows about Scott Summers, as the fate of all humanity might depend on it. More specific, Xavier asks what led the optometrist to the conclusion that Scott was a mutant. Polishing his own glasses, the optometrist says that it was Summers' eyes and the weird glow in them.
A few months ago, Mr. Lamb brought Scott to him because of his recurring headaches and no glasses seemed to help until he finally tried ones containing bits of ruby quartz. These glasses seemed to cure the boy's aching eyes, though the doctor didn't know why. In fact, he wanted to find out today, but evidently Scott ran away before he got to their appointment.
Gazing out of the window, Xavier knows somewhere in the city is a confused youngster, in need of his help. However, he's outside the range of Xavier's mental probes. So lost in his thoughts, the professor almost overhears the optometrist's questions if mutants really are as deadly a threat as the papers say.
(several hours later)
As night falls, Scott Summers jumps off the train he was riding in, not wanting to risk being discovered. He doesn't know what to do or where to go. After all, something happened to him today - causing his eyes to shoot deadly rays endangering a crowd of innocent people. If only he knew what caused the eye beams, or whether they would happen again if he took off the glasses once more.
Right then, Scott recognizes the odor of someone cooking nearby - and he is starved. He follows the smell and, moments later, stumbles in on four, middle-aged, apparently homeless men. Scott politely asks if he can have something to eat, and they invite him to stay with them, asking him if he has run away from home.
Scott mentions how he jumped off a boxcar, but the men don't quite believe him. After all, he is wearing clean clothes and looks like a college student. One of the men even thinks it's a joke, Scott performing some sort of initiation stunt, and he grabs him by the collar, ordering him to give him all his money. Scott says he doesn't even have a wallet, but the four men don't believe him. They pin him down to the ground, his arms twisted behind his back, and search through all his pockets - confirming what Scott already told them. Now really angry, one of the men decides to take off Scott's "fancy sunglasses," so that they could at least clobber them, but he doesn't get to anymore.
Right then, a trio of policemen arrives and the four men spread out and make their escape. Scott is grateful that the police arrived in the nick of time, as he could have hurt the four hobos, even if he didn't want to. However, his troubles aren't over, as now the three officers grab Scott so that he won't run away, as one of them says he sure meets the description of the youngster who has run away from an upstate orphanage. To get a better look at Scott's face, one policeman takes off Scott's glasses, despite the youth's vehement protests. Immediately, the scarlet eye-beams erupt again, but fortunately they only hit the ground as Scott turned his head down in the last instant.
In fear, the three policemen back away from the troubled teenager, and run as fast as they can. They want to get reinforcements to surround the entire area. Scott calling out to them that he means no harm makes no difference. Keeping his eyes shut, Scott ifs effectively blind, but searching the ground with his hands, he eventually gets hold of his special glasses again. Suddenly, he realizes that apparently his own body is immune to the deadly beams, or else he wouldn't even have eyelids anymore. No matter what, Scott knows that he has too run or else the mob will get him, lock him up in a steel cell and label him a freak.
Scant minutes later, overcome with fear and fatigue, Scott reaches a clearing in the woods and notes a shack nearby. Come here, lad... come here. It's almost as if some unearthly voice reaches out to Scott from inside the cabin and, as tired as he is, he sure needs someplace to sleep. Enter, enter. Scott hesitates for a few minutes, but eventually he can't resist anymore and opens the door of the cabin. Inside, there is a man expecting Scott, and he realizes that it was him who called out to him. The man says that Scott has nothing to fear, because he too is a mutant, born to rule.