A few months ago, Operation Zero Tolerance was shut down by SHIELD. Since then, their leader, Bastion, has been held captive and examined by SHIELD agents and the mutated slaves who once worked for him. Outside the base, a shady figure approaches the facility. Bastion somehow senses this person's presence and begins to panic. He commands the agents to free him and that they must escape! The alarm lights go off, but it's too late. An explosion takes place on the facility's perimeter walls that kills many SHIELD agents and the slaves. Within moments all are dead except for the intruder: a big man, covered with armor and carrying a big, sharp sword around. He is DEATH!
In New York's Greenwich Village, Archangel is on the phone, calling Captain Britain to see if Psylocke has arrived safely in England. In another part of the city, Cable practices with his new Psimitar weapon. On the snow covered Mount Everest Nate Grey, the X-Man snowboards carefree. All three men suddenly get a telepathic call-up from Phoenix, who asks for help. She explains the situation: the X-Men have been disbanded by Xavier, and yet are needed. Jean says she has received a telepathic distress call from a young child named Nina whose friends have been kidnapped. With the X-Men disbanded she says begs them to come and help her.
Later at the Institute, Jean is stained from the telepathic summoning, but mainly hopes they arrive quickly. Jean gets her wish, as Archangel and X-Man fly over, leaving only Cable not present. Suddenly, Cable appears behind Wolverine and jokes that he must be slipping. Logan says they are under a lot of stress and that must be the reason why he didn't smell Nate. Cyclops again explains the situation and they decide to leave. Jean sees X-Man hanging back. She goes over to him and asks if it was OK to ask for his help. X-Man tells Jean that she and Scott have always been good to him, and this is his chance to pay them back. He just wants to help.
Cable's a bit concerned about their mission, but Scott says they must do something, as the Mannites are just scared children. The team finally heads off in the Blackbird. As they fly over to the former OZT HQ, Wolverine replies this is the place that Nina told him. Cyclops grows anxious, remembering all the bad things Bastion did to him during Operation Zero Tolerance. Jean asks if he's all right, but Scott replies it's in the past and he can handle it.
After landing, the team proceeds with caution, noting that with the facility burning, someone has gotten there ahead of them. The group starts exploring and wonders who could have done this to the base. As they start searching, Cable asks to Logan why he didn't go his own way when the team split up. Logan answers that no matter what, the X-Men are his family and he didn't want to leave Scott and Jean when things are looking bad.
X-Man, after seeing how well the others work together, notes how easy it is for them all to be a part of a team. Feeling alone, he realizes that he doesn't have a clue how to fit into such a unit. Jean sees how X-Man reacts and asks Cyclops if it was a good idea to pull X-Man into the X-Men's world. Cyclops notes that when the Professor recruited them, they were also just children. Scott recommends that they just give Nate the chance to be a part of something bigger than himself and be a part of a family that he has never known.
When Archangel returns from his aerial surveillance, he informs them that the whole place is deserted, but that something really violent happened recently. Suddenly, Jean catches brainwave activity from inside. She thinks it might be from Nina, but she isn't certain. Scott uses his optic beam and blasts a hole through the wall, which gives the group an entrance to the facility. Jean again senses something, this time a presence. It's malignant. Cold. Evil. Even though she can't tell where it is coming from, Jean tells the team that it is getting closer.
Suddenly, Cable realizes that the ground and the walls are moving and are being manipulated by something on a molecular level! The floor, seemingly alive, begins to attach the X-Men, who defend themselves as best they can. Luckily, Jean finally senses the person who is doing this in the shadows. Logan finds the culprit: He is Headcase, a small green boy with an elongated skull... and a big gun. Headcase threatens Wolverine with his weapon but Nina reveals herself, telling Headcase that the X-Men are her friends, the ones she asked for help.
As Nina leads the X-Men to her other friends, Jean and Cable feel another presence down another corridor, someone full of pain and fear. Nina gets upset and tells them that they should not go down there, and continue on the way she is leading. Jean tells Nina that they have to help the other person in danger too. Nina gets even more upset and says an "evil man" is there. They open the door and discover, to their surprise, Bastion! Bastion's body is gone, leaving only his head, which hangs from a network of cables. Even though he lacks a body, Bastion is able to remain vocal and quips with the X-Men about his situation. Moving the conversation to the Mannites, Bastion explains that when the Mannites are grown up, they will become even stronger then mutants and that the world will then belong to them. Nina starts crying and asks if they can leave and just search for her friends.
The group leaves and Cyclops decides to come back and pick up Bastion after they have found the Mannites. Logan doesn't agree much and wants to kill Bastion for good, but Scott holds him back and reminds him that it isn't the X-Men's way. Nina feels another presence and again gets scared. The group starts their search again and soon finds a titanium door, where the rest of the Mannites are being held. Nina uses her powers and makes a portal through the door, freeing her Mannite friends.
Suddenly the wall begins to heave, as someone begins slicing through. At Cyclops' command, X-Man uses his telekinesis to hold the wall together. Cyclops tells Jean to take the Mannites and get them to safety. Meanwhile he and Cable will go after Bastion. To help their journey, a Mannite suddenly uses his powers to show a plan of the building, which allows Cyclops and Cable to find another way back to Bastion.
X-Man, unable to hold back the force behind the wall any longer, suffers a telekinetic backlash, knocking him to the floor. Sensing that no place is safe, another Mannite, Grace, activates the base's self-destruct mechanism. Headcase tells the group that Grace told the computer to explode. Jean asks Nina if Grace can just stop the computer failsafe, but Nina says Grace can't do that! Jean sends a telepathic message to Cyclops, telling him that the place is going to explode and that they have to return. Cyclops claims he's almost to Bastion, only to find out Bastion's already gone.
Remembering that the Professor said that Nina had teleportation powers, Jean asks her to teleport them away. Nina does open a portal through which Jean, Nina and the Mannites enter. However, when Jean and Nina arrive on the surface alone. Jean asks Nina where the Mannites are, but Nina innocently replies that they didn't want to be there and went someplace else.
Meanwhile, Cyclops and Cable try to find a way out, but the hall they discover is all filled with debris. Scott and Nathan use their powers to blast a way to a ventilation shaft, which leads to the surface. Cable uses his telekinesis to speed his and Cyclops ascent, allowing them to escape. The join Jean and the others, who are already outside and together, board the Blackbird. The jet manages to take off, just as the base explodes.
Jean says it isn't over yet, because now Nina's friends have disappeared and they still don't know who their pursuer was. She asks Cyclops who could have slaughtered the whole base. Even as she poses her question, Death climbs out the ruins of the exploded base. In one hand he holds his sword, in his other... Bastion's head...