In the danger room, the X-Men are training and fighting to survive against various perils, such as spinning buzzsaws and lasers. Xavier and Cyclops are watching from above, reminding everyone to take it seriously as these tests are what they could face for real one day. Xavier then changes the settings so the walls and ceiling of the danger room seem to be coming in. The X-Men try to stop this from happening, but can't.
Storm hates this the most from this as she suffers from claustrophobia and as the walls keep moving in she goes berserk with her powers, putting the others at risk. Xavier turns off the program and things return to normal, but Storm says that she doesn't want to lead the X-Men on missions as her claustrophobia could get her friends into trouble. Xavier tells her that she may have to lead no matter what the situation is. Meanwhile Wolverine is meant to be resting, but he's training as Jean comes in and tells him to stop.
Wolverine suddenly stumbles and as Jean helps him she then says that she has to go, Scott is waiting for her. But Wolverine then says that he is waiting for her, too...Jean goes on without a word. Later that night, she and Scott have been watching a play but Scott hasn't been himself. He admits to Jean that as an X-Man he doesn't want to let Professor X down. Jean knows that he is trying his best, that they all are, and that he needs to loosen up. He says she is right and that from now on he will try to relax. As they are walking down a street they see another mutant, Leech, use his power to bring some fruit to him.
Leech is seen and chased by an angry mob. He leads them down into a subway where some of his friends are waiting for him. Jean and Scott run down and see that some slime is covering up part of the entrance so Jean uses her powers to destroy it.
Inside they find a team of new mutants wrecking havoc on the mob, so Cyclops blasts the biggest guy there -Sunder. After he is sent crashing, the other mutants hesitate but then yet another mutant appears behind the pair and tells them to "sleep".
Annalee has a mutant power that lets her alter other people's emotional states and when she tells everyone to sleep, they do -including Jean and Scott. Callisto, the leader of this band of mutants, then appears and congratulates Annalee before telling Sunder to take Scott and Jean with them as the group go off down one of the subway's tunnels. When Scott wakes up he finds himself strapped to a table.
Leech is also there and thanks him for trying to help earlier. Scott sees that he doesn't have his glasses but his powers won't work at the moment. He is then taken to Callisto, who has been interested in him ever since he attacked the Sentinels. She explains that down here live a group of mutants known as the Morlocks, mutants who have been too disfigured to lead normal lives in the world. Scott explains that his powers come from sunlight and that he won't be much good to them down here. Callisto wants Scott though not just because of his strength, but to provide an heir with her. Scot says no and wants to know where Jean is.
Jean has been tied up but as she is lowered down she breaks free and quickly blasts down all of the Morlocks before linking with the Professor. But as she is doing this she gets knocked down herself and Sunder stops Scott from helping her.
Xavier calls together the X-Men and shows them the place where he thinks Jean was at. Wolverine, Storm, Rogue and Gambit are sent out to the subway to try and find their two missing friends. Storm doesn't like being here due to how cramped it is but she keeps going. They don't see that they are being followed by Tommy, a mutant with a two dimensional power. Not before long the X-Men come across some Morlocks and after a brief fight they run away, so the X-Men give chase.
They come across Annalee who has tricked Jean into thinking that she is her mother. When Wolverine approaches Jean begs for her mother to protect her and she does so by tricking Wolverine into thinking he is covered with scorpions. He sees past this ruse though and gets her to run off after nearly stabbing her head. Jean is left behind and recovers, but she wants to know where Cyclops is.
A door opens up behind them and Callisto reveals that Scott Summers is dead! As Jean runs over to his body, Wolverine isn't convinced and decides he would like to see Cyclops in pieces! Before the others can stop him he lunges at the body!
His claws miss on purpose and hit the ground but it is enough to get the "dead" body moving again, revealing that it isn't really Scott at all -it is Ape, a shape-shifting mutant. The two sides start to fight one another.
Unfortunately there are many Morlocks and one of them, Plague, touches Gambit whilst he's fighting and gives him a fever. Rogue punches her away but Gambit is sick. Storm tells Rogue to take Gambit back to the institute. Meanwhile Wolverine got Callisto to run off and he chases her but he ends up fighting Cyclops instead.
He brings him back to where Jean and Storm are and makes it clear he wants to leave, but Annalee tricks Wolverine into thinking Cyclops is his enemy. He is about to stab him but Jean stops him just in time and also blasts Annalee, ending the spell she had over Wolverine.
Storm then challenges Callisto to a one on one battle. If she wins, the X-Men get to go free but if Callisto wins, she may take Cyclops. Callisto agrees and the two are given double bladed laser swords to fight with. At first Storm is taking hits and Callisto thinks she is too slow but Storm soon turns the battle in her favour.
She knocks Callisto down but says she won't kill her, as that isn't the X-Men way. She offers all of the other Morlocks a chance to return to the surface, as they could come and live at the institute. But they don't want to go up to the surface yet, not until humans and mutants can live together in peace. Storm lets them live with this choice and tells them that Callisto will continue to be their leader.
The X-Men return home and find that Gambit is recovering well, he will soon be better. As Xavier thanks Storm for doing such a good job as leader of the team in this mission, Scott and Jean go to thank Wolverine for his help, only to find his room empty and near a window is a picture of the two X-Men split in half! To be continued...
NOTES
There are several other Morlocks in this episode but I'm not naming them all, most don't even have any lines.