Though Jay Leno has concluded his opening monolog, the sound of laughter dies out in the Xavier Institute for Higher Learning when a pounding on the door cuts through both laughter and the sounds of a stormy night. Colossus, armored up, opens the door, ready for an attacker, but instead finds a badly beaten, yet beautiful, woman dressed in a tattered green dress. The woman falls into Colossus’ arms and asks him for help. Colossus is surprised to see Callisto, the woman he once believed he loved, but alas this appears to be just another night at the home of the X-Men.
Colossus brings the bloody Callisto into the foyer, where Professor Xavier, Storm, Jean Grey, Iceman, Archangel and Bishop all arrive, some ready for battle, others ready for sleep. Upon seeing the injured woman, the Professor sends Jean to prepare the med-lab. Storm flies overhead and asks Colossus who the woman is. Despondently, Colossus replies that none of them would recognize the woman, because they were not there when she became a victim of Masque. The woman is Callisto.
Annoyed, Iceman asks why he always feels like he just walking in on the third reel of a movie. In a condescending tone, Bishop tells Iceman that maybe he should spend less time perfecting one-liners and spend more time preparing him for any eventuality. He would last about five seconds in the XSE. Telepathically, Xavier tells both men to be silent. Xavier then questions the weak Callisto if she was attacked by the Marauders again. Weakly, Callisto explains that, if he can believe it, it was her own people who did it. The Morlocks attacked her. However, they should not worry about her. It is more important to save the Healer. Bishop and Archangel go outside and find a badly beaten man near death on the front lawn.
In his room, Mikhail Rasputin wakes up from a horrible nightmare. Today, like every day, he thinks about the horror that becomes his life. Mikhail sits shirtless on his bed and looks at the dead bodies on the floor around them. Mikhail addresses his fallen comrades and asks if any of them heard the commotion downstairs, or is he just crazy? From behind, the High Avatar asks Mikhail if that is not a trick question. The dead cannot hear him, because that is what they are: dead. They are dead because they trusted him, because he killed them. When her father ruled these people they were his slaves but they were also alive. Mikhail puts on his shirt and tells the High Avatar to taunt him if she wishes like she has every hour since his return to Earth. He knows, however, that he did his best. Putting on his boots Mikhail leaves the room.
In the med-lab, the X-Men are all in their uniforms. Jean tells Xavier that both Callisto and the Healer are stabilized but they should rest undisturbed until the morning. Xavier explains that, under normal circumstances, he would agree. However, if the Morlocks have gone mad as Callisto suggested and if they would try to kill one of their own, then time may be of the essence. Tired, Callisto tells Xavier to use his telepathy to enter her mind. He should be able to learn all he needs to know. Charles touches Callisto’s hand and tells his students to prepare themselves. He links all the X-Men together so they can experience every though and feeling that Callisto did.
The X-Men are then presented the events that occurred earlier in the evening to Callisto. An hour ago, Callisto returned to her apartment, only to find the Healer. She threatened to kill him for breaking in but the Healer apologizes and explains that he came for help. As she knows, Masque took leadership of the Morlocks from Storm and re-engineered their minds and bodies, which drove all the Morlocks insane. Masque is now dead and the Morlocks are guideless. Angrily, Callisto accuses the Healer of confusing her with her old self. She no longer has any concern for those “pathetic monstrosities.”
Suddenly, a large group of Morlocks burst through the walls and scream that Masque was right; pretty Callisto no longer cares for them. She used to love them. Callisto kicks away one of the Morlocks and tells them that she cared until she was transformed and could walk among the humans that once scorned her. While some Morlocks attack the Healer, several others grab Callisto and tell her to lead them. She resists and one of them gouges out her right eye. Callisto refuses to give up everything she has for them. She kills one of the mutants and tells them that she created one of the Morlocks and she can destroy them too.
The visual ends and Xavier explains to his students that Callisto barely survived the encounter. Expecting a second wave of attackers, she came to the school for sanctuary. The X-Men must take initiative, however, to end the cycle of violence so they can save the Morlocks from themselves. Mikhail tells the Professor that he is overreacting, which surprises the team, mostly because he was not in the room a moment ago and because he was not included in the Professor’s mindlink. Colossus tells his brother that he should be resting for their trip to Russia. Mikhail reminds his brother that the trip is not until the morning. However, he could not leave having failed to stand up for Callisto’s kindred spirit. She is a fellow shepherd who has lost her flock.
Shocked, Jean asks the Professor how Mikhail was able to enter his psychic loop. Telepathically, Xavier tells Jean that he does not know and that there are many mysteries about Mikhail. Out loud, Xavier announces that their patients need rest. They should continue their discussions outside, but telepathically adds that they should do so out of earshot of Callisto and the Healer. The X-Men leave the room, Mikhail giving one quick look back at Callisto, who smiles back at him.
In another room, Storm tells Charles that there is nothing to discuss. She is leader of the Morlocks and it is her responsibility alone to deal with this. Angry, Archangel tells Storm to come off it. He is the direst result of her so-called leadership over her people. When he was with X-Factor, he lost his original wings defending the Morlocks. Appalled, Storm asks Warren if he really blames her for his condition. Warren explains that all of them are guilty for not giving the Morlocks the attention they deserved. They are living in a mansion, while horribly disfigured mutants are scavenging beneath the streets of New York City. Storm explains that the Morlocks chose that for themselves. While the X-Men argue, the Healer gets up from his bed and stumbles over to Callisto, on whom he uses his powers.
Xavier tells his students to stop arguing. They seem to have more pressing problems to deal with. He then ushers his X-Men into the med-lab once again. Bishop asks why, but is cut off by a scream. The X-Men rush into the room and Colossus wonders if that was Callisto screaming. Bishop tells Colossus that it wasn’t. Callisto is gone and, instead, there is some vile, loathsome creature.
The X-Men find the Healer dead on the floor and Callisto, back in her original form, standing in front of him. Callisto tells Bishop that she is the same person who was in the room before. The Healer used the final measure of his power to heal her. It wasn’t nearly enough. All he did was return her body to its normal state. Her wounds are healed, at least, which will be a regret of the Morlocks when she finds them.
In Arlington, Virginia, a man enters the Eden Park Nursing Home. An obese nurse rudely orders him to stop and tells him that the visiting hours end at eight. The man replies that he was referred to this institute by a mutual friend of theirs. The woman tells him that she has no friends, mutual or not, but stops and asks if he meant friend with a capital “f.” She apologizes and leads him down a corridor and into a room where a skinny, blond man is strapped to a chair. The visitor looks at him and tells the nurse that he doesn’t look like humanity’s last hope. The nurse explains that he doesn’t but that is where faith comes in she supposes.
Below the streets of Time Square, the X-Men, including Xavier but minus Iceman, travel through the Morlock sewers. Bishop voices his concern over having the Professor come with them but Xavier tells Bishop that he was taking care of himself before any of his X-Men, with the exception of Wolverine, were born. He will manage. Worried, Jean thinks to herself about how, before the Professor’s spine was shattered, he rarely joined them on a mission. Is he coping for his loss by overcompensating?
As the X-Men continue down the sewer, Bishop is startled to see a large poster on the wall warning them about the radiation levels. Remembering having seen the poster before, Bishop tells Storm but she dismisses his claims and assures him that it is one of many posted throughout the sewers to discourage the curious. In front of them, Colossus brags to Archangel about how he thinks Mikhail was able to tap into the Callisto’s thoughts through an undiscovered psychic link that exists between him and his brother. Archangel sarcastically tells Colossus that it is fascinating and asks to be wakened when they reach Morlock central.
Suddenly, the X-Men stop and Colossus announces that they have arrived. Bishop orders the Professor behind him but Xavier quietly tells Bishop that he won’t be going anywhere. All present are shocked at the sight of a large pile of dead Morlock bodies. Archangel checks the pile to confirm that they are all dead and Jean points out that she cannot even pick up psychic residue. Astounded, Colossus wonders who could have committed such an atrocity. Telepathically, Xavier tells his students that no one did. While he cannot pinpoint the exact nature of the illusion, it is clearly the work of an emotionally disturbed Morlock.
The X-Men charge the pile of bodies and run right through. Archangel realizes that this was just a sick attempt at a “Do Not Disturb” sign. The X-Men emerge on the other side of the illusion, to be greeted by another horrible sight. Bishop pulls out his guns and realizes that, if this is a sign of the Morlock madness, then it seems that their assistance will be looked up as favorable.
Jean is horrified and is hardly able to say out loud that the Morlocks are destroying themselves. Indeed, the disfigured mutants are all attacking each other, some choking one another, while others fight with large pieces of cement. Archangel swoops around and tells Jean that they have to stop them, even if it means taking the Morlocks down hard. Bishop agrees and Xavier tells his students that they may have to use a greater show of force to win. However, he wants to try every peaceful alternative first.
Back at the mansion, Callisto threatens to rip out Iceman’s spleen if he does not release her now. Iceman looks at the woman, strapped to a bed for her own safety, and asks if the sedatives wore off. He sympathizes with Callisto but having her skulk around in the sewers won’t help anyone. Calling Iceman an idiot, Callisto screams that she wants to see those “ungrateful freaks” pay for ruining her life. Mikhail agrees with Callisto and orders Iceman to let her go. Defensively, Iceman ices up and tells Mikhail that he cannot do that. Mikhail, being the larger man, towers over Iceman and tells his friend that he is afraid that they have a problem.
Back in the Morlock Tunnels, Xavier senses that the Morlocks are all linked together somehow by some unbreakable grip of psychic turmoil and mental agony. For the moment, Masque’s legacy has left him unable to help the Morlocks. Worried, Colossus asks Xavier how the X-Men can stop the Morlocks if they cannot be psionically sedated. Dominatingly, Storm announces that, after all that has happened recently, she is still their leader. One way or another, they will listen to her. She powerfully walks to the Morlocks and thinks to herself that her words were hollow. The Morlocks owe no allegiance to her. Leadership of the Morlocks, like her relationship with Forge, was sacrificed to secure her position with the X-Men.
The Morlocks stop attacking each other and look at Storm, who wonders if Forge was right about her not having a life outside the X-Men. Is it right of her to lead people when she has no clue where her own life is heading towards? Storm begins to cry and hopes that the Morlocks are not suffering because of her ambition. Several of the mutants grab Storm and ask her if she, as their leader, will help them. All the Morlocks begin to beg Storm to help them. As the Morlocks begin to surround her to beg for help, Storm is overcome by fear, as her claustrophobia takes control of her. Above in Time Square, the rain begins to pour harder in reaction to Storm’s mood.
As Storm tries to escape the crowd to collect her wits, a Morlock wraps its tentacles around her leg, trapping her. Storm tells the Morlocks that she will do what she can but begs for them to give her room. The Morlocks do not listen and overcome Storm, who freaks out. Enraged, Bishop tries to help Storm, who desperately tries to fly into the air. Every fiber of Storm calls out for freedom.
In the streets above, the people of New York are caught in winds of hurricane ferocity. Suddenly, a massive bolt of lightning hits the street and creates a crater. Storm flies out of the crater, screaming that she is free. The Morlock who wrapped himself around Storm agrees with her, as he is free as well. So are every other Morlock. They are all free forever. The Morlocks rush out of the crater and take Manhattan.