In their Blackbird jet, they X-Men speed away from the former base of Operation Zero Tolerance, which has just been obliterated in a nuclear explosion. Wracked by the massive electro-magnetic pulse of the explosion, the jet's navigational computer and controls are shot.
Piloting the plane, Wolverine remembers aloud that they have lost too many Blackbirds recently and this one is staying intact. He asks Jean, Cable and X-Man to assist. Working together, the trio uses their telekinesis to hold the plane together while Logan continues trying to land safely.
Suddenly, Nina senses Death outside and starts panicking. Death attacks and again, shooting bolts out of his sword at the plane. Nina explains he is the evil man she was talking about earlier and that he is after her and her friends and is trying to kill them. Cyclops tells Wolverine to land the Blackbird some distance from their foe as they are going to need time to set up their defenses. After sarcastically asking Cyclops if he would like fries with that order, Wolverine complies, successfully landing the plane.
Once on the ground, the group goes out. Cyclops orders Archangel to fly recon and for X-Man and Cable to set up a defensive perimeter. Jean tells Cyclops she'll guard Nina, with her life if necessary. Wolverine gets angry, telling her that it will never come to that; he'll kill their foe himself. Jean asks Nina for information. Who would want to hurt her friends, where did the others go when they disappeared? Too scared to think straight, Nina is unable to remember. Having no other choice, Jean uses her telepathy to go into Nina's mind, in the hope of helping her remember. Nina recalls that Xavier did the same to her, once before, and says it would be fun.
(in Nina's mind)
Jean enters Nina's mind, and sees her transformed. No longer a girl of flesh, Nina is techno-organic. Nina finds it funny to see Jean surprised, and explains this is the way the Mannites look, in reality. Jean asks if Nina knows what a Mannite is and where they come from. Nina innocently answers that a Mannite is her, Darco and the rest of them and they come from home. Nina tells Jean to turn around, as Jean gets even more surprised. She sees a technologically advanced room filled with machinery beyond description. Jean asks to Nina if it is OK to enter deeper into her mind, which Nina agrees saying that it is more fun than being back in the scary place.
As they travel deeper into Nina's mind, Jean and Nina are stopped by shadowy representations of the other Mannites. They tell Nina they can't let other's know of their existence. Nina explains that Jean is a friend, but the Mannites claims she would be just as scared of them as 'He' is and that they'd all kill them if they knew where they come from, and knew who they're parents are.
Suddenly, something happens with the Mannite Darco, who screams in pain. Nina starts panicking, and says Darco is going through "the Changing". Severing the telepathic bond, Nina brings herself and Jean to the real world.
(back in reality)
Excitedly, Nina tells Jean that they must help them, and have to go now! Jean informs Scott that they have another problem. A short time later, Jean has explained what she learned from the Mannites. Realizing that they don't have time to repair the Blackbird, Cyclops decides to split the team up. One team, consisting of himself, Cable and Archangel will hold back Death while Wolverine, Jean and X-Man take Nina to the other Mannites.
After Cyclops and Jean kiss and say goodbye, X-Man uses his telekinesis to fly them to the Mannites location. Cyclops notices something is bothering Cable and asks if something is wrong. Cable explains he comes from a horrible future and that he has come here to prevent it from happening. He fears Death is part of something much bigger than the Mannites and that they must find and stop Death before her finds the kids, no matter what.
Using her senses, Nina directs X-Man and his telekinetic bubble to a small town. The town, and the carnival it seems to be hosting, appears to be deserted. Immediately, upon landing, Wolverine notices a strange, black gooey substance that it is covering everything. After admitting that he cannot identify the substance, he and Jean heard X-Man's call. X-Man has discovered the inhabitants of the town, all of whom are covered in the goo. Wolverine tries to cut them loose with his claws, but it doesn't really work. A little frustrated, he notes to Jean that the nearby machinery that is also covered in the goo is breaking down its metal and plastic components. He also notes that it wouldn't be too pretty if the goo broke down organic material as well as inorganic.
Jean asks to Nina if this is part of the 'changing', which Nina thinks it is.
Nina explains that the change is different each time and when it completes, they become something... different. Already trying to use her own telekinesis to remove the goo, Jean tells X-Man to use his own telekinesis to help. A little lost in thought, X-Man notes that their situation seems a bit too familiar to him and it reminds him to his former world. He says that the Mannites want to be left alone, and asks Jean why are the X-Men hunting them down. Don't they deserve a chance to make it on their own? Jean answers that they are not hunting the Mannites, but are trying to help them. She says they want to make sure they stay alive long enough to make their own decisions. X-Man, still not convinced, saying that if it's true that the Mannites have been made in a lab, something he is familiar with, then everyone has always made their decisions for them. He says that the Mannites will have to learn to take care for themselves one day, sooner or later.
Suddenly, the other Mannites appear behind the X-Men. Scared, they beg Jean to help them. They claim that Darco is going through the Changing, and they must run. Jean tries to calm one of the Mannites and get more information, but he is nearly incoherent. He claims that the change is the "baddest of bad things" and is why Bastion was so afraid of them. He point to Darco, just emerging into sight, and says that they must all run before his Changing hurts them all. Wolverine and X-Man, getting a bad feeling about the transformed boy, advise Jean to get the others to safety. Jean says that Darco is still just a scared kid, no different from any of them when their mutant powers kicked in.
Meanwhile, the other team still searches for Death. Touching the ground, Cable says he can feel Death, and he must be nearby. Cyclops tells Cable that he sounds like Jean when he talks like that. Cable jokes that it must a telepath thing but Cyclops says it's more than that, and believes Cable knows it as well. He reminds Cable that he is their son, no matter how strange it is. Wanting to change the subject, Cable tells his father that now isn't the time to rehash family history. Changing the subject to their foe, Death, Cable notes that he is much more than he appears to be. Their conversation is interrupted by Bastion.
Alive, but still lacking a body, Bastion has survived the explosion, no worse off than before. Humorous in tone, he explains the X-Men were never really tracking Death, they were being baited by him. Bastion claims Death is prepared all too well, anticipating their every move. Bastion also tells Cyclops that he should have let him kill him, as it would have avoided much suffering. Bastion says they will never see Death coming. Cable says that Bastion is right and feels that Death is still coming closer to them, closing in. Cyclops tells Cable to create a mindlink between him and Archangel, who's still on his aerial recon. Suddenly, Death appears from out of nowhere and attacks Archangel, who is still airborne. Over the telepathic mindlink Archangel tells Cyclops that Death must be using a cloaking device.
Meanwhile Jean and co continue their fight against the goo, which now has begun to fight back. Slashing tendrils with his claws, Wolverine tells Jean that one of the things he loves about her is how much she cares for everyone. He explains he also feels sorry for Darco, but his powers are also bringing the villagers in danger. He says to Jean if she can't help Darco, they'll have to do it his way. Jean tells to Logan to sheathe his claws and says she thinks she knows how to help Darco, but first she must know more about the Changing. Jean uses her telepathy to build a link between her and the other Mannites to learn what Darco's powers are.
Jean begins to understand. She tells everyone that Draco's powers allow him to absorb organic and inorganic material and convert that into energy. However, whatever is happening inside his body demands more and more energy. The tendrils, she says, are manifestations of his powers and his body's instinct to save itself. Jean tries to go deeper in the Mannites mind to understand where the Mannites come from and suddenly says that she understands. She is interrupted as she is captured by one of Draco's tendrils. Wolverine and X-Man are quick to react. X-Man tries to free Jean directly with his telekinesis while Wolverine cuts the tendrils at their source. Once freed Jean tells them to stop immediately, as she wants to handle it her way. She now knows how to stop Draco.
At that moment, Cyclops and Cable stand searching the skies, having lost contact with Archangel. Suddenly Archangel appears, falling to the ground, unconscious. Cyclops and Cable run take care of Warren who warns that Death is too powerful and wants something from one of them. Noticing something behind Cable, Cyclops opens his visor and shoots behind Cables shoulders to a shadowy figure. Death effortlessly blocks the beam with his sword, leaving Cyclops aghast.
Wolverine warns Jean that they have no idea what this will do to her, but Jean calmly replies that neither he nor she has a choice. Using Nina's connection to other Mannites, and covered by Wolverine and X-Man, Jean uses her telepathy to reach Draco. She tells Darco to relax and that the Changing is not a bad thing, but a natural one. It is his fear that is making it more painful and makes his powers run out of control. Using her telepathy, Jean and Nina go into his mind. The three are engulfed in blinding light, from which a Phoenix bird appears. When the light subsides, Draco is sealed in a luminescent cocoon.
Nina asks Jean what has happened to Draco. Jean explains that Draco manifested the cocoon on his own; he just needed help to calm enough to allow it. She further explains that the cocoon appears to be a natural manifestation of his powers. Mannites, she says, go into a chrysalis state while their abilities develop. When Wolverine asks what will happen when he comes out, Jean replies that she doesn't know.
Elsewhere, Cyclops and Cable continue their fight with Death. Despite their simultaneous attacks, they do not seem to be able to do Death any harm. Needing help, Cyclops telepathically contacts Jean, who quickly explains that she has found more than they bargained for. When Cable realizes that Death is taking an interest in Cyclops conversation with Jean, he orders Cyclops to break contact. Too late, Death's trace is complete and he vanishes before their eyes. Cable curses himself, realizing that Death was only engaging them long enough to get a lock on the others. Whoever he is, Cyclops says, he's studied their moves inside and out.
Cyclops, Cable and Archangel return to the Blackbird and return to the skies. Archangel, piloting the jet, warns Cyclops that the Blackbird sustained extensive damage from the electromagnetic storm and he doesn't know how long it is going to hold together. Reassuring his teammate, Cyclops points out that as long as they have the plane, they have the advantage. Unfortunately for Cyclops and his group, they are unaware that Death clings to the fuselage of the Blackbird, traveling with them to Jean's group.