Deep within a hollowed-out mountain fortress in the heart of Europe, a strangely helmeted figure sits in front of a huge screen and views images of the X-Men's first battle with the Juggernaut. Talking to himself, he ponders the question why, and how the X-Men were able to defeat this foe, the ultimate personification of power, and not only once but twice.
Several minutes of watching later, the strange man decides that he has seen enough. The scenes he reviewed have shown him everything he needs to assure Factor Three's victory over the X-Men. Thinking that they were rather fortunate to extract these images from the captive Professor Xavier's memory, the helmeted figure contacts some other operatives of his mysterious organization. The screen now displays Magno-Disk One, an egg-shaped, flying object outside the mountain. The helmeted figure asks whether they are ready to attack and, addressing him as "Number Two," the craft's two pilots confirm that they will reach the impact area within moments.
A few miles away, and drawing nearer to this "impact area," the five X-Men are aboard a plane in their civilian identities. Looking at the many mountaintops below, they wonder how they could pinpoint the exact location of Factor Three's headquarters, but when the stewardess passes them by they fall quiet. It's too late, though, for she has overheard part of their conversation and curiously asks what this "Factor Three" is that they were talking about. Being the quick thinker he is, Hank comes up with a fast cover, and pretends that it's a new ingredient for liquid detergents - surely she must have heard of it. The stewardess denies that, though she admits that she is too busy to watch TV.
While Warren thinks to himself how he both admires and envies Hank for his wits a bit, Jean and Scott are talking to each other in the next seat. Jean says that she hopes they reach the airport soon, for she is sick and tired of keeping up the act of cheerful college students on a vacation, when Professor Xavier is in danger. Just as Scott tries to cheer her up, the plane gets caught in a momentary downdraft.
Suddenly, there's an explosion outside the plane and looking out of the window, the five teenagers see the egg-shaped flying object tailing them at an incredible speed. They immediately know that it's no conventional plane and as such it must belong to Factor Three. They are in for the kill it seems, for the plane would have been caught in the explosion if it hadn't been for that downdraft right before the attack. Reasoning that Factor Three obviously knows of them being aboard the plane, and that Factor Three are willing to kill the entire passengers and crew just to get at them, Scott knows there is only one decision to make. In order to save the plane, the X-Men have to leave it.
Indeed, the pilots of Magno-Disk One are already circling around, this time wanting to ram the plane instead of just blasting at it. Using his increased strength, Hank manages to open the cabin door, and the five mutant teenagers jump out, with Scott yelling at Hank to grab his waist, just like he did Warren's. Now that they have dived out, the flying egg-shaped object turns, and starts blasting again at the five teens.
Still holding himself to Warren with his one arm, Scott uses the other hand to lift his glasses and fire an optic beam straight at their attackers - with some unexpected result. Magno-Disk One blows up. Scott never meant to destroy the ship, just to disarm it, but considering that they were willing to murder innocents, he doesn't waste too much pity on them. Hank surmises that Factor Three must have been so confident of their craft's speed that they never bothered to give it sufficient armor.
One crisis solved, the X-Men find themselves in another - namely, they are plummeting to their death. Scott looks around for Jean and Bobby and eventually spots them several feet away, holding onto each other, with Jean trying to telekinetically slow down their descent. Scott then turns his attention to Warren, who he is still holding onto and starts ripping his jacket and his shirt, so that he can reach the harness that holds his wings.
However, right then Scott's glasses are being blown off and, while he closes his eyes just in time to harm nobody, the X-Men's leader instinctively reaches for them and accidentally lets go of Warren. Still in free-fall, Scott is now all by himself and effectively blind, as he doesn't dare open his eyes. Even worse, Jean sees that there's a pinnacle below, and Scott is headed right for it. She shouts a warning, but she is too far away for Scott to hear her.
By now hanging on Warren's right foot, Hank has fortunately noticed Scott's peril too, and he grabs the suitcase that Warren has been holding in his hand the whole time. With a couple of back-flips in mid-air, Hank manages to get over to Scott, however he doesn't have enough momentum to do anything else but reach him. It looks like the certain doom for them both, them only being a few feet above the pinnacle, when Hank has another idea.
Grabbing Scott's head and directing it at the danger below, he tells his leader to open his eyes. As soon as his eye beams erupt, Scott sees the grave danger himself and wonders whether his force-beams will be able to clear their path in time. Naturally, they do, and as Scott closes his eyes again, Hank realizes that this has bought them only a few moments. They are still about to impact.
Nearby, a small miracle occurs. Warren flexes his wings, and it was hard enough for them to snap through the straps and his clothes. Now able to fly, he quickly crosses the distance to Scott and Hank and grabs them left and right. Hank asks about Jean and Bobby, who are still falling nearby, and the two remaining X-Men have followed everything their teammates experienced.
In no time, Warren has reached them too, but now the team faces the fact that the winged mutant can't carry the weight of five people. Scott suggests for Warren to let go of him, but Warren wants nothing to hear about that. He asks Jean to provide some telekinetic help, but the redhead has already exhausted her limits, slowing down herself and Bobby the way she did. Jean fears that they'll all be killed.
Bobby says that it looks like it's up to him then and the others are a bit surprised, as they don't see how his ice powers could help them. Having no time to explain, Bobby ices up, and creates a huge sliding board, to ease the team's descent towards the ground below. Hank helps Scott slide down, as he is still helpless while he keeps covering his eyes. Jean even says she that sliding down would be fun, if it weren't for the danger. Bobby having had only so much time, the slide ends somewhat abruptly, and while they still come down a bit hard, none of the team is seriously hurt. A split-second before he hits the dirt, Scott already orders the rest to get into their costumes, earning him a snappy side-remark from Iceman, that there is no other deputy leader who could bark out orders even while he's toppling through the air.
Within minutes, the X-Men have changed into their costumes, when the Beast hears a strange humming sound behind them. Turning around, they see a spider-shaped robot, just like the one that Spider-Man recently mentioned to have fought. Avoiding one of the robot's rayblasts by getting airborne, Angel tells the team that this solves one of their problems - it seems that they no longer have to search for Factor three, as Factor Three has found them first.
Using her telekinesis to turn the device's ray-blast arm against itself, Marvel Girl manages to make the robot destroy itself, however it was just the first of about a dozen such robots. They have the X-Men surrounded from all sides, with two hooded figures standing behind them. They call out to the X-Men to stay where they are, for they are now prisoners of Factor Three.
Cyclops orders his team to remain calm, for he wants to learn what their game is, and the two Factor Three operatives continue their speech. They declare all attempts at escape useless, and say that the X-Men's only hope of survival is to join Factor Three in its battle against the humans. Otherwise, they will be smashed like everyone else opposing Factor Three. The X-Men are given an ultimatum of ten second to make their decision.
Not willing to give in, Iceman thinks he has found an escape route when he spots a ledge behind them, leading further downwards along the mountainside. However, just then two of the mechanical spiders make their way up the ledge, warming up to blast at the team. Fortunately there's a tree standing right above them, and Beast swings around one of its branches, kicking both spiders down the hill, one with each foot.
The X-Men make a run for it, well aware that none of the other spiders are firing at them, as if Factor Three wanted to herd them along this way. Still, not having any other options left, Cyclops hopes that this is not the case, and blasts the ledge behind them, so that the spiders and the Factor Three operatives can't come after them. After all, while they want to find their missing mentor, they don't want to end up his fellow prisoners.
Around the next corner, though, the X-Men find the ledge leading into some deeper valley that's entirely covered with some white mist. The mutants don't like the looks of it, but have no other choice but to run through. Second later, jean is the first to get very tired, the white mist apparently containing some sleeping gas, apparently a trap set by Factor Three. Angel was flying above the mist, but seeing his friends in distress, he dives down, trying to pull them out, only to end up feeling the gas' effects too. All of the five mutants struggle as hard as they can, but it's no use and they fall asleep. Scott's last words before succumbing to the darkness are that it must not happen like this, for there is no one else to strike back at Factor Three in time.
(an unknown amount of time later)
Mere minutes or an eternity later, the unconscious X-Men are lying on the cold, hard floor of a dark room inside the mountain fortress, entrapped in an invisible force bubble. They slowly come around one by one, awakened by a voice that's belittling them. Barely able to open his eyes, Cyclops asks himself why that voice sounds so familiar. The villain responds that he can easily find out by looking up, and he'll know the true meaning of fear.
Hovering above the defeated X-Men are four monitors, each one displaying the face of one of their former enemies: the Vanisher, Unus, the Blob and Mastermind. The Vanisher, who was talking before, makes room for Unus and the Blob's gloating, the latter saying that seeing them helpless was worth the wait and the holding back from any attempts of personal revenge. Telekinetically probing the invisible barrier surrounding them, Marvel Girl knows he is right - the X-Men are helpless.
While Angel is still surprised how these villain got to Europe, after all when last seen two had been stripped of their powers and the other two were hiding in America, Iceman already comes up with the idea that they must have been the bosses of Factor Three all along, when he suddenly noticed movement on the wall at the other side of the room. Wearing a purple and pale blue costume, the strangely helmeted figure appears on a small platform that's connected to a doorway high up in the wall with a small staircase. Hovering above him there's a second platform shrouded in shadows, with another figure sitting in its center, behind several panels and control elements.
Taking in the entire sight, Cyclops wonders whether one of these two unfamiliar men might be the true head of Factor Three after all, and he demands for an answer regarding what they did to Professor Xavier and the Banshee. The helmeted figure reminds Cyclops that he is hardly in the position to give orders, but for now he is willing to forgive the team's deputy leader's arrogance. Still, he warns the quintet that they are before a court of law, and anything they say might be held against them.
Scott gets a bit angry with the villain, acting as if they were defendants in some trial, to which Beast says that he suspects that this is precisely what they are. Finally introducing himself as the Changeling, their prosecutor, the helmeted figure, confirms Beast's comment. He reveals that in best traditions of Western jurisprudence, the X-Men shall receive a fair trial with all evidence duly weighed... and then they shall be destroyed.
The five mutants are taken aback, unsure whether they can take this seriously or not, if it wasn't for the danger and their being trapped. Cyclops asks what they are accused of and, trying to taunt the Changeling into revealing what his mutant power might be, he also asks him if he is the real leader of Factor Three or just some hired stooge. Pretty annoyed, the Changeling answers that he is no stooge but in fact second in command of Factor Three, preceded only by the Mutant-Master.
Just as Scott asks who or what this is, he notes an overhead grid of lights starting to glow, revealing the silhouette of the figure sitting on the second platform. Also wearing a distinguishing but entirely different helmet, the Mutant-Master begins to speak. He reveals to the astonished team that they are accused of betraying the cause of their fellow humans by acting as friends of the Homo sapiens, and for that they must die.
With mad-ridden, wide-open eyes, the Changeling tells the X-Men that they are honored, for few mortals have been privileged to even hear so few words from the master. With that, he says they have wasted enough time already and, pressing a button on the control panel in front of him, he makes the four video monitors combine into one. On the screen, there's an image of Xavier and the Banshee, both unconscious and held in stasis tubes elsewhere inside the fortress. The Changeling tells the X-Men to behold at these two helpless pawns who have lured them here, once they could have been Factor Three's most valued allies, but now they are all doomed.
Jean is glad to see the two prisoners alive, whereas Cyclops is concerned, knowing that they can't expect any help from them. After switching back the monitors so that they display "the visages of those who are both witness and jury," the Changeling declares the trial open.
The Vanisher is the first to testify, and he finds it only fitting that he gets to start, for he was also the first to battle the X-Men right after their initial encounter with Magneto. Images and sounds from the team's fight with the Vanisher are being displayed on the video wall, as the villain explains how he, time and again, tried using his mutant power of self-transportation to escape from their grasp, only for them to continue siding with the humans against their own kind. Additionally, it was them and their accursed professor who robbed him of his memory for so long, which can only be classified as treason against the race of homo superior.
Unus interrupts the Vanisher's speech, saying that they don't have all day for this trial and that it's now his turn. While the X-Men are still in disbelief at the mental images of their former battles being brought up as evidence against them, the screen now showing scenes from their battles with Unus, the untouchable foe describes his experiences with the mutant teenagers. It was the Beast who tricked him with a dose of a booster ray, increasing his powers so much that he couldn't touch anything anymore, not even food, forcing him into surrendering.
The Blob is up next, starting with that he couldn't care less for what the X-Men did to the others, though they will be sorry for ever tangling with him. Iceman suggest for him to return to the carnival where he belongs, tough the Blob is unimpressed by the frosty mutant's bravado - after all he has a score to settle and he always pays his debts. In fact, the Blob feels that he owes them more than anybody else, for the X-Men beat him three times. Still the final victory will be his, and for that alone the Blob is happy to have joined Factor Three, even if it wasn't going to make them rulers of the world.
Finally, it's Mastermind's turn to speak, and he starts with saying that he can only imagine their surprise for seeing him again. During their last encounter, Mastermind had been turned to stone by the mysterious Stranger. However, the spell wasn't a permanent one and, as soon as it had worn off, did Mastermind search for other mutants like himself, only to find them among Factor Three. Still, nothing could erase the indignities he had suffered at the X-Men's hands, which count many more than those three defeats of the Blob. As a member of Magneto's Brotherhood of Evil Mutants, Mastermind fought them numerous times, always close to victory, yet always defeated. But now he can avenge those defeats by voting for the X-Men's and Xavier's destruction.
With that, all four villains reach their decision, and cry out a single word numerous times "Guilty. Guilty. Guilty." The monitors go blank, and the Changeling sums up that the X-Men have been found guilty by a jury of their fellow mutant, guilty of the crime of betraying the cause of homo superior. For that, he, as the prosecutor, asks that they are being given maximum penalty - that of death. Rather frustrated, Angel and Marvel Girl express their opinion on this "kangaroo court" that has tried and condemned them without allowing them to speak on their behalf.
The Changeling orders them to fall silent, so that they can hear the verdict of the judge, a.k.a. the Mutant-Master. The team looks up to the shadowy figure on the hovering platform, who declares that before pronouncing his ultimate verdict, it would please him to let them in on how Factor Three intends to achieve complete world domination.
"Too long has the inferior species called Homo sapiens held sway on this planet! Now, the time has come for the mutants of the world to rule! But, before this may accomplished, first there must be a total destruction of the power of the human race to resist - a destruction achieved by means of their own mightiest weapon - the hydrogen bomb! Yet, atomic weapons alone are not enough to completely humble the accursed humans! There must be a world-wide war - war such as this planet has never seen! And, we shall accomplish this holocaust by the simplest of means...
Soon, at a top-level meeting of iron-curtain officials, an explosion shall occur - a fatal blast that shall be blamed upon the United States. At almost the same time, the air filtration system of an American ICBM base will carry a potent paralytic gas to every man there. With the base's personnel reduced to abject helplessness, my mutant followers shall unleash a deadly rain of atomic missiles - aimed at the heart of the iron curtain - and, in that moment World War Three shall have begun - and the human race shall be doomed!! And, in the carnage that remains, we - the third factor between east and west - shall seize power! That is our destiny - a destiny which you, because of your treason - cannot share! Thus, I sentence you to utter oblivion."
The Mutant-Master instructs the Changeling to carry out his sentence, and he eagerly responds. The Beast still tries to convince him that they can't destroy all humans just because of their mistrust for mutants, but it's too late. A push of a button activates a stun charge ray gun, rendering the five mutants unconscious once more, allowing the Changeling to prepare an apparatus called Oblivio-Ray, which is meant to carry out the verdict.
When the X-Men wake up a short time later, they find themselves strapped to this machine each of them wearing a headgear that is meant to sap their wills, so that they will become loyal agents of Factor Three. Before leaving the chamber, the Changeling declares that their fate will be a life-in-death.
Once they are alone, the X-Men try to get free. Scott asks Jean to try using her telekinesis on his visor, but she finds the device over his head too tight for her to do anything about it. Never giving up, Cyclops has another idea and has Bobby form several icicles with his fingertips, even though the youngest X-Man has no idea what the use is. Next, Scott orders Jean to levitate the icicles above the machine they are strapped to and hold them in place. It's no easy task directing them accurately from her angle, but the redhead manages to do it and, after a while, the ice begins to melt, the water dripping into the machine, short-circuiting it. The bonds automatically spring open and the X-Men are free again, only Scott is still wearing a metal band across his visors to block his optic beam.
Just as Marvel Girl tries to help him getting it unlocked, she and the rest of the team notice a giant robot entering the room, apparently sent to guard them. The Beast can't help but describe the expression on its face as hostile, and indeed it starts firing at them, armed with both a machine gun and a flame-thrower. The X-Men scatter, and Jean levitates Scott to safety.
Angel circles around the robot, trying to draw its fire and distracting it, allowing Iceman to encase the flame-thrower arm in a block of ice. Beast leaps around, finally landing on the antenna on the robot's head, destroying its visual sensory input. By the time Scott gets his head free, the robot is already firing blind, and with a well-aimed blast he completes what the Beast start, destroying all its sensory mechanism. While still firing at random, the robot poses no longer a danger, as it walks off into the opposite direction, away from the mutants.
Trying to avert the Mutant-Master' plans, the X-Men rush back into the chamber, where the mock-trial was held, only to find it empty - there being no sight of either the Changeling or his superior. Fearing that mankind is doomed if they can't find them, the X-Men receive an unexpected answer from the huge video screen.
The image of the Mutant-Master appears, saying that they are correct. While they may have escaped the Oblivio-Ray, they are helpless and too late to stop the inevitable destruction of mankind. Within the hour, an explosion of runaway missiles will signal the end of humanity and the coming of power of the evil mutants, all under the Mutant Master's rule. The X-Men are left in despair, what can they possibly do - trapped inside the enemy's fortress, with so many Factor Three agents on the loose and time running out...