An exhausted Danielle Moonstar slumbers over her desk. Charles Xavier comes closer her. Normally, he would never hurt her. If his mind were his own. But it is not.
In the still of the night, while Xavier slept, something sinister, spectral, absolutely evil crept into his mind and took over. He is no longer Charles Xavier, but the Entity. The Entity thinks to himself that he and Charles are the same, two sides of the same coin, manifestations of the same mind; Xavier light and reason, the Entity his nasty side all darkness and decadence. What pleasure, Charles denies himself, he muses, being surrounded as he is by such pretty young playthings.
Dani wakes with a start at his mental touch and screams, as psychic fingertips play a sensual caress across her soul. She does not scream long, however, before collapsing to the carpet in the throes of indescribable pleasure. Liked that, did she? the Entity leers. Yes, Dani agrees no longer in control of herself. Drawing her closer, the Entity promises to reward her with more of the same if she is a good girl and will aid him in dominating the New Mutants.
Within the Microverse, the X-Men and the Micronauts have just escaped from the Entity’s dungeons with not much of a plan. Escape, locate the source of the Entity’s power and eliminate it, is all Storm has to offer.
Somewhere above them on the cliff, Baron Karza, in the shape of Kitty Pryde, waits. Karza believes to have stopped the Entity once and for all by slaying his corporeal form. With that accomplished, he no longer needs the X-Men or Micronauts and intends to shoot them.
Wolverine was a soldier and a spy before he was an X-Man and his battle senses are acute. Moments before Karza shoots, he warns the others of a sniper and Colossus quickly shields Commander Rann from a deadly blast. Nightcrawler instantly teleports up to disarm the sniper, only to find that it is Kitty. Karza phases away, leaving Kurt to believe that the Entity twisted Kitty even more than he did the other X-Men.
The next moment, the landscape shakes, as Thorium torpedoes are loosened on the planet, courtesy of Kitty Pryde in Baron Karza’s armor and Karza’s battlefleet. Her goal is to stop the Entity at any cost. Looks like they caught the Entity napping, she announces to Chief Scientist Degrayde. Degrayde is deeply suspicious of his master’s behavior. Though he battles the Entity, as he must, Karza has shown an uncharacteristic concern for his soldiers and sadness at the loss of life.
However, before Degrayde can fathom his master’s newly found humanity, Karza suddenly cries out ‘Professor X,’ seeing briefly Xavier’s astral form. Kitty announces that her plans have changed. Degrayde is to suspend the assault. Degrayde protests and Kitty tells him to be silent, as she teleports away to the planet below. A pity that someone will forget to order an end to the bombardment, Degrayde thinks with a smirk.
In the Entity’s palace, Karza, in Kitty’s body, has returned, cursing his luck. He is not familiar enough with the X-Men’s abilities to slay them. Kitty, in Karza’s body, appears, grabbing Karza with her armor’s glove. At that moment, the X-Men and Micronauts break in, only seeing Karza threatening their teammate. Kitty protests that they don’t understand, which they summarily ignore, until Professor Xavier’s voice is heard in their heads, telling them that things are not as they seem.
Xavier animates the Entity’s slain body and explains that Kitty has changed places with Karza. The heroes are unsure whether to trust this information until Wolverine points out that the real Kitty could have easily phased through Karza’s hand. And, while his mind is inhabiting the Entity’s rapidly failing lifeform, Xavier continues, he fears their enemy is on Earth.
The Entity, in Xavier’s body, admires Cerebro, the device meant to amplify his psychic power. Multiplied by Cerebro, what might he do? He‘ll try destroying the Microverse, he decides.
The planet is still being bombarded by the fleet, despite the orders Kitty, as Karza, gave. Degrayde’s doing, Karza suspects. He must have seen this as a chance to replace him as supreme monarch of the Microverse. Rann concentrates on trying to re-establish his mindlink with the Bioship and succeeds. The Bioship comes and gathers them up, laughingly evading the shots of Degrayde’s fleet.
Suddenly, though, Fireflyte screams in pain, announcing that something is attacking the Enigma force. Should the Entity breach the Spacewall and destroy the Enigma Force, the Microverse itself would be destroyed. The frontier worlds are the first to fall under the psionic onslaught. It locates Karza’s battlefleet and destroys it. Chief Scientist Degrayde dies, his dreams of conquest unconsummated. The rest of Karza’s armies also perish, leaving only one force standing between the Entity and the death of the Microverse and the Bioship’s shields are barely holding.
They must cross the Spacewall to reach Earth, but the ship can’t do it without dropping his shields. They’d all die instantly. Fireflyte reminds them that the Spacewall is a construct of the Enigma Force. She is one with that force and can sing them through the Spacewall. She does so and the Bioship passes through a rift in space to land before Xavier’s mansion.
As the Bioship lands, the X-Men realize, for the first time, that it is alive. They have known living spacecrafts before - the Acanti - but at least they looked alive, whereas Bioship looks 100 % robotic. Rann explains that Biotron was one of the first 6000-series organic roboids. He was not so much made, as born. He died… and his memories were resurrected in this living Bioship.
Acroyear anxiously points out that Fireflyte’s light has dimmed. She has come close to singing her self out. Karza, who has dressed Kitty’s body in a new costume - much to the real Kitty’s chagrin - cynically points out that hers will not be the only song snuffed out, should they fail to stop the Entity.
Suddenly and savagely, the Bioship is struck from behind. A sneak attack launched by Cannonball. Scarcely have the heroes inside the Bioship recovered from their surprise, when the staggering spacecraft again comes under assault by the rest of Xavier’s New Mutants. Sunspot and Magma both attack, talking about their adoration for the Entity. The diminutive heroes leave the Bioship and, together, Colossus, Acroyear and Huntarr manage to heave Sunspot into Cannonball, while Storm asks if Bioship can restore them to their normal height. The damaged ship replies it wishes it could, but that would drain what little power it has left. Power that at the moment is barely keeping him and the Professor alive. Storm understands and flies off.
Inside the ship, Nightcrawler struggles to keep the fast-failing Charles Xavier alive. Xavier asks Kurt to tell Bioship to save its healing for itself. This body he inhabits should die eventually, but not yet. He requires two things. First the X-Men and the Micronauts have to keep their foe’s attention on the battle, no matter the cost. Secondly, Nightcrawler is to keep his shell alive until Xavier tells him otherwise. Then, he is to let nature take its course. If necessary he might even have to kill him.
Outside, the heroes are having trouble. Not only are they small, they also have to pull their punches against the New Mutants. The Entity focuses on the New Mutants and doesn’t dare to carry out the planned destruction of the Microverse at the moment.
Elsewhere, Magma’s lava attack badly damages the Bioship and Nightcrawler wonders what to do. Xavier can’t help him. His mind has left the body and wanders through the mansion. He finds Illyana Rasputin guarded by Lockheed, unconscious but otherwise unharmed. Xavier notices surprised that Lockheed senses his astral form. Suddenly, the dragon flies off and roars. Apparently, Kitty is in danger. Xavier nears his study, where his body, Cerebro and the Entity await.
Gathering up his courage, Charles Xavier guides his astral form into the maze that is his own mind. A psychic phantom, he does not see his brain as a surgeon might, all pulsing organic matter, but rather as a hall of mirrors, each mirror a thought reflecting another thought or memory. Memories such as the original X-Men reporting for duty, the Sentinels, the new X-Men fighting Mystique’s Brotherhood, the Brood, his first sight of Lilandra, Magneto, Dark Phoenix. That memory gives him pause. The Entity has violated this private place and must be excised, he grimly vows.
Outside, Lockheed roars at the New Mutants. Kitty, in Karza’s armor, orders him to scatter the X-babies, not hurt them. How does she know that the creature isn’t itself under the evil influence of the Entity, Karza asks. Lockheed senses the true Kitty Pryde, but he carries his loyalty too far, as he attacks Karza in Kitty’s body with flames.
Unaware of what’s happening in his mind, the Entity wonders what’s going on. He wasn’t able to destroy or control Lockheed and, now suddenly, he tries to kill his mistress. He finally understands that a bodyswitch between Karza and Kitty has taken place. Not pleased with having anything hidden from him, the Entity selects the perfect revenge, as he takes over Kitty’s and Karza’s minds, trying to force them to painfully kill each other.
Why doesn’t he just snap his finger and have them drop dead, Kitty wonders. Is it more fun that way? Xavier understands that, while this is the case, another reason is that there, unlike the Microverse, the Entity’s power is limited to affecting reality on the astral plane. He cannot destroy them physically, only seize their minds and force them to do the job themselves.
Karza’s gauntlets are choking Kitty’s body and Karza finds himself unable to phase free of them, even while the Entity is forcing the two of them to phase together. Trying to help, Fireflyte sings. And Kitty and Karza scream. Suddenly, the Entity finds pain inflicted on himself as well. There’s someone in his mind.
Outside, thanks to Fireflyte’s song, Kitty is back in her body while Karza teleported away.
The damaged Bioship tells Nightcrawler to take the Professor and flee. Magma’s heat is getting to great. He cannot maintain any internal life support systems, including his own. Kurt is in a quandary. The shock of teleporting might hurt the Professor’s weak form, but the heat of the lava will, so teleport he must.
On the astral plane, Xavier notes the Entity’s body dying. He has to act now. He begins his psychic assault on the Entity’s thoughts, which have taken root in his mind. Moments later, the Entity appears in his armor. This time, the battle is different, though, for Xavier is willing to sacrifice his own body, risk his own death, if only it will stop the Entity. The Entity senses pain and Xavier tells him hat he has caused a stroke, which will either kill him or completely destroy his cognitive functions. The Entity shrieks, as Xavier’s body slumps over.
At that moment, the mortally wounded body of the Entity disappears from Nightcrawler’s arms. The New Mutants are themselves again and they quickly find the unconscious Xavier.
The Micronauts have no reason to cheer, though: their Bioship is dying, the X-Men are still small and the Micronauts are trapped on Earth. Fireflyte offers that she can sing them back to the Microverse but they must hurry. Even now, the Enigma Force is closing the Spacewall, forever closing the Microverse off from Earth.
Bioship states that he has died before and it was rather peaceful. He asks the Micronauts to return and carry on their fight, just as he restores the X-Men to carry on theirs. The heroes wish each other farewell and the Micronauts vanish.
Xavier awakes moments later, explaining that he deceived the Entity by making it believe he was initiating a massive stroke, in essence a game of “chicken.” The Entity fled to his own body, which by then was dead, so it ceased to exist. He only wishes he could atone for his atrocities. Their battle may be over, but the Micronauts’ still continues.