Cyclops and Xorn, carrying the unconscious forms of Lilandra and her advisor Araki, run through the Shi'ar Superdestroyer starship, which is exploding around them. Following his friend and ally, Cyclops, Xorn asks him if he has no doubt that they can survive this. Stiff faced as always, Cyclops tells him none at all. Further, Cyclops informs Xorn that he is carrying the single most important woman in the galaxy and that Xorn is carrying her guru, Araki. As a side note Cyclops tells Xorn that Araki gives very good advice and he would probably enjoy talking to him. Entering a larger chamber, the two X-Men see the Ship's transit streams. Cyclops tells Xorn that the streams are thought guided so he must think about the Xavier Institute. Still carrying their unconscious charges, the two jump into the transit stream and disappear.
From the grounds of the Xavier Institute, Cassandra Nova, clad in the body of Charles Xavier points to the exploding starship in Earth orbit. Asking if they can see it, Cassandra tells the Superguardians that it represents the end of galactic civilization. Grasping a helpless Gladiator with her psychic grip, Cassandra tells him that the system he served is now in ruin and its figurehead is insane. Declaring the most powerful of the Superguardians a failure, Cassandra tosses him aside and calmly walks toward the mansion.
From the hedges next to the greenhouse, Angel and the Beak watch Cassandra. After declaring the events spooky and sick, Angel asks who the "Baldie" is. Beak continues trying to tell Angel that the headmaster is a good guy. An evil old woman is using his brain and will kill her [Angel] for laughs. Putting everything together, Angel realizes that she is the woman responsible for the millions killed in Genosha. Next, taking a stab at pessimistic prophecy she tells Beak that the "space psycho" is going to hand it to them on an ass-shaped plate and eat their brains. Using morbid humor of his own, Beak tells Angel that Cassandra would throw up if she ate his and would cut her own throat if she had to be him for more than five minutes. Nearby, Stuff pleads to Emma Frost not to hurt him. Cross-armed, Emma instructs her wards, the Stepford Cuckoos, to do as she taught: swing him merrily from a psychic gibbet and braid his thoughts until they ooze. Sensing that Stuff's morphic record and copy functions are online, Emma holds out one hand and asks the girls for the tissue sample they have acquired.
In the bowels of the mansion, Beast looks into Jean's blood-tear filled eyes and asks if it is her in there. Jean tells Beast that she is fine and has stored the professor's entire consciousness in her own memory. Suddenly speaking with Xavier's personality, Jean addresses Beast as Henry and is surprised that he has changed again. Beast suggests that they check Jean's blood pressure but is rebuffed by the Xavier's controlled Jean. Xavier tells Beast that Cassandra is here and they must deal with her once and for all. Jean strides confidently through the Institute halls toward the Cerebra chamber and passes the Institute's students. One student, Frida, addresses Mrs. Grey-Summers and asks if Cassandra is going to kill them all like the people in Genosha. Dismissing the fears of the student, Jean tells her that she will not. When another student asks if they are going to kill Cassandra, Jean tells her that they will have to think about that. Turning her attention to the Beast, Jean tells him that it seems the obvious solution, but it goes against everything that they have ever believed. There has to be a better way.
On the ground level above them, the immense front doors of the mansion implode, throwing Wolverine to the ground. Wracked with pain, Jean clutches her head in agony and screams that Logan is down. Gradually losing coherence, Jean tells Beast that she is losing Charles. Babbling, she says that she can't remember the smell of soap at his grandmother's house, or how good it felt to overcome the monster Onslaught. The twelfth birthday party is gone, along with a nice day with Moira. Cradling the helpless Jean, Beast yells to the students to get to safety and asks if he has to start roaring at them like some Leonine Martinet. Resolute, the students tell Beast that none of them are going to hide with the humans in the Danger Room. Cassandra killed their people and now wants to kill them. Deciding they no longer want to run, they tell Beast that he can't stop them from defending themselves. It is the way their teachers taught them. Jean pleads with Beast to not let them go. Almost inaudibly, Beast asks somebody, please, to help them.
Two forms of pure white light fill the hallway blinding everyone. When the light subsides, Xorn and Cyclops, carrying Lilandra and Araki, stand before the group. Cyclops quickly hands Lilandra to someone else and asks Beast if Cassandra has arrived yet. Jean stretches out her hand and tells her husband that he is her favorite super hero, to which Cyclops replies that he loves her too. After picking up his wife, Cyclops asks Beast to bring him up to speed. What is wrong with Jean and what is wrong with him? Beast informs Cyclops that they were infected by microscopic Sentinel machines from the Ecuador Master Mold, which are resistant to every antibiotic he has tried. Beast tells him that Cassandra has made them sick to weaken them and it is a miracle that they are still alive. Pointing to Jean, Beast tells him that she has Septicaemia and could go into toxic shock and die.
Unwavering, Cyclops tells Beast that he doesn't believe that and neither should he. Entering the Cerebra chamber where Cassandra's body lay, they find Xorn at Cassandra’s body. Probing Cassandra's body with him powers, Xorn informs Cyclops that she is dead. Cyclops begins to grow enraged, reminding Xorn that he told him that he could bring the professor back. Turning to the collapsed form of Jean whom Cyclops has lay in a chair, Xorn tells Cyclops that his task is now clear; he is there to heal her. Xorn places his hands on the sides of Jean's head, which begins to glow with blue energy. After the energy subsides, Xorn tells her that the Sentinels in her blood stream are all dead. After Cyclops tells Jean that they are going to be all right, Xorn tells Cyclops that he is next, and then Beast. The strongest first, while there is still time.
As Xorn heals Cyclops, Beast looks at Cassandra's corpse and wonders aloud what she is and what they are dealing with. Healed by the touch of Xorn, Cyclops admits that he feels better. Sometimes one just doesn't know how bad they feel until the feeling's gone. Beast informs Cyclops that he was dying of blood poisoning. In answer to Beast previous musing, a rejuvenated Jean tells him that Cassandra is what the Shi'ar legends call Mummudrai which is a type of Yin to a Yang. Legend, she continues, is that each of us faces their own personal Mummudrai in the womb shortly before birth. It is our first experience of the alien, the other... the different. She asks him imagine a bodiless parasite species, born without flesh or real substance. Cassandra, she explains, is Charles Xavier's Mummudrai. She copied his cells to build a body and accessed the full spectrum of latent mutant functions in his genome.
As Xorn heals Beast, Jean, speaking with Xavier's personality, tells them that he felt Cassandra monstrous thoughts and her raging hunger, vast enough to consume the world. Lashing out in their mother's womb, his first conscious act was a murder attempt. Though born dead, the Mummudrai survived as chaotic cellular matter. After forty years, he explains, of clinging to a sewer she was strong enough to walk free. Xavier tells them that it was his original sin. His flaw. His failure. Putting the Cerebra helmet on Jean's head he tells them that Cassandra wants to reach Cerebra. Through Cerebra he/she explains, Cassandra can control the minds of the entire mutant race and wipe them all out at once. Sensing Xavier's plan, Cyclops tells Xorn and Beast to remember that Cassandra is in the professor's body. Confuse and disorient her, but do not hurt her.
In the foyer of the mansion, Cassandra confronts the recovering Wolverine. Towering above the X-Man, Cassandra offers him a deal; if he takes her to Charles, then she will let him survive as a soldier-drone. She tells him that it is her best offer... and then address him as James. Unflinching, Wolverine tells Cassandra that her telepathy will not work on him when he can switch to pure instinct. Beast arrives to provide Wolverine with help, but the two are attacked by the Institutes students, under the control of Cassandra. Watching the two defend themselves against their students, Cassandra tells the two X-Men that she will humiliate and annihilate them all. Suddenly the room fills with blue light, and from behind his metal mask Xorn tells Cassandra that he will not let her hurt or humiliate anyone. Throwing himself through her psychic aura, Xorn grabs the body of Xavier and proclaims that he can heal her. With Cassandra distracted, Beast, with a syringe in each hand, jumps onto Cassandra and injects her with their contents. Seemingly unfazed, Cassandra repels Beast and throws Xorn to the ground. Ignoring Wolverine and the students, she leaves them and heads to the bowels of the Institute. Quickly, Beast realizes that the students have been freed from Cassandra's mind control. As if in answer to the unasked question, the Stepford Cuckoos stand in the doorway telling the students to stop it.
In the Cerebra chamber, Cyclops tells Jean that Cassandra is coming and implores her to self-destruct Cerebra. Jean disagrees, telling him that it is their last chance. The consciousness of Xavier, she tells him, is too strong for one mind to contain, but maybe she can use Cerebra to split him... and hope that he survives the ordeal. As she voices her plan, mutants around the world look into the sky and sense something. Taking the helmet off, Jean tells Cyclops that she thinks that it worked. Even her memories of what she has done with Xavier are gone. Her words do not even register with Cyclops, however, as he collapses under the power of the just arrived Cassandra. Moving toward Jean, Cassandra orders Jean to give her Charles... and her body. Defiantly, Jean tells Cassandra that she thought she would be scared of her, but is not. Angrily, Cassandra slaps aside Jean with her psychic aura's "hand" and enters the Cerebra chamber.
Placing the Cerebra helmet on her/Charles' head, Cassandra tells Jean that she will use Cerebra to amplify her thoughts tenfold and directly access the minds of every mutant on the planet. She will then turn them against on another. However, as she touches all of the minds Cassandra senses one mind in particular: that of Charles Xavier. Still recovering >from Cassandra's blow, Jean tells her that she just remembered what she forgot; that she broke Xavier's consciousness into pieces and stored a little part of him in every single living mutant mind. These minds were just waiting for Cassandra to connect them all back up. In the Cerebra chamber, Cassandra begins to howl in pain, feeling like white-hot claws are tearing through her head. Through the pain, Cassandra hears the voice of Jean, or more correctly, Phoenix. A fiery Phoenix raptor surrounds both Jean herself and the entire Institute.
Now expelled from the body of Charles Xavier, Cassandra stands as a being of pure psychic energy, bodiless and blind. Telepathically, Jean tells Cassandra that she is not welcome in their Xavier's body or in this world. Not while she is there to protect it. Xavier, now returned to his own body, lifts the Cerebra helmet off of his head. Yelling to Phoenix, he tells her that he is back and the Mummudrai is loose. With gritted teeth, he tells her they have to strike while she's helpless.
Staggering aimlessly in her psychic body, Cassandra's speech begins to degrade. Through her nearly incoherent muttering, she begs for a body. In answer, Emma Frost arrives from the corridor. Clad in her protective diamond form, Emma holds the limp form of Cassandra's old body. Addressing Cassandra, Emma tells her that she has her body and is willing to trade for it. Before offering the deal, Emma tells Cassandra to check the body's DNA to be assured that it is a living breathing, real deal. While she does so, Emma tells Cassandra that she knows that she can't stop something like her, but surely they can still bargain. With a dry, tight smile Emma tells Cassandra that if she lets her and her girls live, the body is all hers.
Horrified, Beast yells to Emma that if Cassandra gets back into her own skin, she's practically invulnerable. Holding the massive Beast back with his arm, Wolverine tells him to just hold it. Nearby, Emma approaches Cassandra's psychic form and tells her that she had better do it before she changes her mind. In broken speech Cassandra says that she understands Emma's need to live. Her mind is all shiny, a reflection like prism. Still aghast, Beast says to Cyclops that Emma has just betrayed them to a genocidal maniac. Once a villain, always a villain. As a dry afterthought, he asks if someone will please act worried. In response, Cyclops tells Beast to calm down and think about the situation.
Accepting Emma's deal, Cassandra's psychic form engulfs her old body. Her assimilation complete, Cassandra's flesh-body opens its glowing eyes. Instead of springing to life, however, Cassandra gurgles. After a moment, Cassandra manages to address Emma, who holds her body. In a semi-mechanical voice Cassandra asks Emma what she has done. Dryly, Emma tells Cassandra that she has reduced her to the status of a pocket calculator and suggests that she consider it her just desserts. Still in Emma's arms, Cassandra's physical body begins to lose its form. Turning briefly amorphous, Cassandra's body eventually settles to that of the Superguardian Stuff.
(inside Cassandra's mind)
Cassandra peeks through her fingers, which have been covering her face. Now wearing the old female body she wore for so long, she sits in a classroom filled with orange chairs and desks. In the desk behind Cassandra, who is sitting in the front row, is the monstrous psychic form she manifested while inhabiting Xavier's body, which now struggles with a pencil and paper. Still taking stock of her surroundings, Cassandra asks Xavier, who is sitting behind the teacher's desk in the front, what she is doing. Xavier dryly replies that Cassandra must be new here. Still trying to sort everything out, Cassandra asks what she is... and how come she no think good? Jean, who was sitting next to the door, rises and addresses the pupil. She tells her that it is okay. This is a school and she is here to learn. Turning to the blackboard Jean begins to draw a large "X". Meanwhile, Xavier picks up the apple on his desk and tells his pupil that they will be starting from the beginning. "A is for atom", he begins.
Emma continues to carry Cassandra's Stuff body, which mutters "B is for bomb". Emma informs the group that Cassandra is trapped in a synthetic brain, programmed to learn. She tells them that they all have her girls to thank for the eleventh hour plot twist. The children, she says, were a revelation. Taken aback at the plan, Beast apologizes for his "once a villain" statement. Finally having a moment to themselves, Cyclops asks Jean if she is okay.
From within the Cerebra chamber the X-Men realize that in body and soul, Xavier has returned to them. Addressing his X-Men, Xavier asks God to bless them all and then tells them that he feels like a very, very long lie-down. As Xavier begins to move in his seat, Beast tells to not try to get up as he has his chair. Stepping out of the Cerebra chamber under the power of his own legs, Xavier thanks him, but says that it seems that he won't be needing his wheelchair any more.