In the Danger Room Storm, Jean Grey, Gambit, Rogue and Jubilee are in the middle of a practice session. Suddenly, all hell breaks loose as several animatronic weapons spring into action. The X-Men use their various powers to evade the dangers. Jean Grey becomes cocky as she easily hurls away two huge saws flying at her through the air. However, she is almost killed as another approaches behind her. Storm swoops in just in time to save her with a whirlwind. The Professor speaks to them over the megaphones. He reminds them of what happened to their teammate Morph and that they must take these dangers as seriously as those they might encounter in the field. Storm gives each of the X-Men different orders as the Danger Room is activated again. Then, all the walls in the room begin to move closer and the ceiling begins to fall as well. Storm tells the others to stop the walls, and that she will slow the ceiling. She creates a gust of wind in an attempt to stop the roof but it doesn’t work. The others are also unable to stop the walls. As the room gets smaller and smaller, Storm begins to panic. Finally, when she is wedged between the floor and the roof, she completely loses control of her emotions. She creates a hurricane inside her the room. Pushing her teammates against the walls. Finally, she collapses, having momentarily exhausted her powers. The Professor projects an astral image of himself to the X-Men. Storm states that she does not wish to lead as her claustrophobia places the others at risk, but he tells her that it may not be a matter of choice when the time comes.

In his room, Wolverine is practicing his martial arts. He is still wearing a bandage from Sabretooths attack. Jean appears in the doorway dressed to go out. She tells him that he should be resting. He brushes her off; he is still practicing when he feels a stab of pain in his stomach. Jean rushes to his side. There is an intense moment between them as they stare into each other’s eyes. Jean breaks contact, stating that Cyclops is waiting for her. Wolverine says that he is waiting for her too.

Later, Cyclops and Jean walk out of a theater. They have just seen Phantom of the Opera. Jean comments on how detached Cyclops was. He tells her how important it is to him to be an X-Man. Jean tells him that he needs to relax for the good of the team. Nearby, a young boy peeks out from behind a street vender. His skin is green, and it is covered with scales. He reaches out his hands and fruits from the vender float through the air toward him. Someone sees what is happening and yells that the boy is a mutant. Instantly, a crowd forms, wanting to attack the boy. The boy uses his powers to separate them so that he might run through.

The mob pursues him and Cyclops and Jean realize that they have to help the boy. The mob makes its way into the subway tunnels and is met by a band of mutants. One of them is dripping gray ooze and hurls tendrils of it at the people. He has also coated the floor behind them with it. He causes it to rise until it has formed an impenetrable wall behind them. Cyclops and Jean arrive behind the wall. Jean uses her telekinetic powers to make a hole in the wall. She and Cyclops soon realize that it is the mob and not the mutants who are in danger and begin to defend the humans from the mutants. Unnoticed by anyone, an old woman approaches behind them; she begins to speak in a tone that echoes through the room. She repeats over and over again that she must sleep. But instead, it is the humans who fall asleep. Cyclops and Jean are among them. A woman wearing an eye-patch appears behind her. She refers to the woman as Analee and states that she’ll be rewarded.

Back at the mansion, Wolverine lies on his bed looking at a picture of Scott and Jean. In the hallway Gambit and Rogue walk by, asking where they are. Gambit says that they deserve a little time to themselves. Wolverine pops one of his claws and scars Cyclops’ chest on the photo. Back in the tunnels Cyclops waked up in a cell. He isn’t wearing his sunglasses but his eyes are normal. He sits up and finds the young scale faced boy they tried to save earlier. He thanks Cyclops and states that he is responsible for the loss of Cyclops powers. He refers to himself as Leech. One of the mutants who attacked the humans appears in the door and forcefully takes Cyclops to an open area. Here, the patch-eyed woman we saw earlier meets him. She introduces herself as Callisto and as leader of the Morlocks. She explains that the Morlocks are composed of mutants who are too deformed or whose powers are too dangerous for them to live above ground.

Behind her are several television screens. She turns them on and a tape of Cyclops begins to play. Images of him blasting Sentinels appear and she states that she wants him as her mate. Cyclops argues that his powers will be no god to her as sunlight fuels his power. She points out that she does not need a protector, instead she requires an heir, so as to better serve her people. He tells her to take out an add and begins to inquire about Jean. Callisto yells that he refuses her and commands Sunder, the mutant who removed him from his cell, to destroy Jean. Who has been suspended from the roof in chains. She is also blindfolded. Once she has been hoisted to the ground Jean lashes out with her telekinetic abilities. She uses them first to free her of her restraints, then to attack Callisto and the rest of the Morlocks. She yells telepathically that Scott is her date. Momentarily gaining the advantage in the fight, she attempts to telepathically contact the Professor. He receives a broken that they have been captured before she is silenced.

He gives the X-Men a rough pinpoint of their location and they set off to find them. Storm, Gambit, Rogue and Wolverine enter the Subway tunnels and Storm asks Wolverine to lead the way. Unbeknownst to them, they are being followed by a woman whose hair is all the colors of the rainbow. She appears to have been invisible, but when she turns her head she is revealed to be as thin as a sheet of paper.

They are still walking when Sunder and the mutant who oozes goop attack them. Sunder grabs Rogue while the other mutant traps wolverine and Gambit in his ooze against the wall. Storm pursues Sunder and blasts him with a lightning bolt until he releases Rogue. He escapes and they follow. They craw; through a narrow passage and Storm is obviously having a hard time. Gambit states that she’s not going to make it and that Wolverine must help her. He in turn says that he will help when she asks for it.

They come to a door, Storm uses her powers to open it and they find Jean and Analee behind it. Analee has used her hypnotic powers to convince Jean that she is her mother. Wolverine attempts an attack, but also falls victim to Analees powers. She convinces him that he is covered with scorpions. However, he is able to break free of the hold long enough to knock her unconscious. Jean snaps out of the spell as well and inquires about Cyclops. In the distance Callisto stands over the fallen body of Cyclops. Across his chest there is huge scar and she states that they mourn his passing. Jean begins to cry, but Wolverine moves toward Cyclops’ body and offers to take him back to the surface in pieces. He pops his claws and despite the protests of the other X-Men sticks them into the ground on either side of the body’s head. Suddenly, Cyclops wakes up, and that of a Morlock shape-shifter replaces his features.

Wolverine states that he could smell that it was not Cyclops who had died. Storm and the X-Men react by engaging the Morlocks in battle. Wolverine goes for Callisto, who uses her staff to compensate for his claws. During the course of the battle an old woman, who causes him to break out in a fever, attacks Gambit. Rogue punches the old woman across the room, but it is too late. Storm commands Rogue to get him back to the mansion immediately. Callisto places a kick in Wolverine’s stomach and runs off. He pursues but stops when he passes Cyclops door. He states that he might make a couple of women very sad at that moment, but that he can’t bear to see Jean cry. He carry’s Cyclops back to the others. Behind him, Callisto is pleased at the knowledge that he loves Jean Grey as they might use that to their advantage.

Meanwhile, the X-Men continue to fight the Morlocks. As Wolverine approaches with Cyclops, Analee turns her powers on Storm, making her feel as if she was in a small space. Wolverine is next. She makes him believe that were it not for Cyclops Jean would love him. Wolverine is about to kill Cyclops when Jean interjects. She blasts Wolverine away while trying to reason with him. Analee attempts to convince him that Jean is forcing him to love her, but he can’t bring himself to hurt her. He collapses and Jean blasts Analee.

Callisto tells the Morlocks that they must kill the X-Men one at a time until Storm agrees to leave Cyclops behind. Instead, Storm gets up and states that she and Callisto shall settle the fight. The terms of the duel are Cyclops and leadership of the Morlocks. Knowing that she would lose the respect of her tribe if she refused, Callisto accepts. However, she states that Storm may not use her powers in any way. Storm agrees and they are handed brightly colored batons. They engage in a duel and at first Callisto has the upper hand. However, Storm eventually manages to defeat her. However, she does not kill Callisto, instead she offers them safe haven at the mansion. However, the Morlocks refuse. Storm states that she will return to them when humanity accepts mutants. Until then, she appoints Callisto to rule in her place.

Cyclops wakes up and asks Jean what happened. Back at the mansion, the X-Men are gathered around Gambit’s bed. The professor states that he will make a full recovery. He also turns to Storm and congratulates her on the mission. She states that the entire team nearly perished. But he says that they didn’t, and that he believes Storm to be responsible for that.

Cyclops and Jean go to Wolverine’s room to thank him but find that he is gone. On the floor, lay the remains of the photograph he was looking at earlier. It has been sliced in half.