At night time in Warwick, New York, the screams of a child calling for her parents are heard from inside a house. The parents race through the doorway and the mother startlingly questions what the matter is. A boy and girl are in beds, side by side, while the girl tells her parents that her brother, Billy, is scaring her. Billy denies the accusation as the mother attempts to calm them down. She leans to the girl and hugs her as she admits that they scared the life out of her. The father sits on the boy‘s bed and asks Billy how many times he has told him not to scare his sister, especially before bed. Billy again tries to deny the matter but once again the girl states that he was in fact scaring her and was telling her about monsters. The father looks at Billy and questions him on the subject matter.
Finally Billy admits that the was telling his sister, Wendy, how the government has monsters under their control that can come for you in the middle of the night and snatch you out of bed. He knows this because his friend Brian Smitty from school was telling him about it. Wendy smiles in acknowledgement of her telling the truth. Their father scolds Billy and tells him that he is surprised that his boy can be taken in by such a story since government controlled monsters are only an urban legend. He tells Billy that he has to be smarter than that but Billy tries to convince his father that the stories are true. The mother pulls the covers on the girl and tells Billy that it is plain nonsense and that Wendy should have nothing to be afraid of because she knows there is no such thing as monsters. On cue there is a loud crash as Kane, Wild Child and Sauron crash through the kids bedroom window which easily startles the family.
Billy realizes that his parents are wrong, as there are monsters and they are here right in front of them. The three Weapon X agents reach out their hands to the family and mention something about government business. They asked the family not to make it any harder and to come along quietly. However the father them on what this was all about. The three agents explained that it was about acts of mutant terrorism. Mr. Taylor admits that they are mutants, but not terrorists like they saw on TV. Billy knows something is wrong and senses that his dad feels it too, which is probably why he tells his family to make a run for it, while he holds off the Weapon X agents. The father builds up some kinetic energy between his hands in an attempt to hold of their unwanted guests, while the others run, but the family turns in mid stride as they hear the screams of their father. Suddenly they come to a slamming halt and are thrown to the floor. The three look up in amazement and realize they could have gotten away if the monsters hadn't brought along their friends. Blocking the doorway are the Washout, Marrow, and Sabretooth.
The mother reminds the kids that even they had been taught to always hide their powers unless it was a very dire time. This qualifies as such a time, and they should fight it with all they have. The mother and children's eyes begin to glow with power. Billy knows that his mother and Wendy are scared, and he is trembling too, but still they were ready to fight. However, the second three set of agents part the way and Mesmero enters. He only needs to speak a few words as the family looks into his eyes, and they submit themselves to the unwelcome visitors.
Billy awakens to find that he is dizzy and confused and staring at a strange set of eyes. Frightened, he latches on to his father while Wendy is safe in Mom's arms. Billy questions what these weird slug-things are before realizing that they belong to a blue guy who is sitting right next to him. As Billy looks around he realizes that they are sitting in a plane with other travelers. Individuals who make the blue guy with two giant slugs look not so weird. The blue guy turns out to be a pretty cool fellow named Maggott, who apologizes for the spook his slugs gave Billy and tells him that they are just as scared as everyone else. Nobody has a clue as to what is going with the exception that the lot of "mutant terrorists" are being transported somewhere on some type of airship. Maggott holds Wendy's face in the palm of his hand and remarks that the thought of a cute little kid like her being labeled as a mutant terrorist is funny. Maggott then states that this many mutants arrested together couldn't be a good thing. As Billy looks out of the plane window he begins to see Maggott's point as the area in which they are headed appears to be some sort of prison camp.
While the passengers are escorted off the plane, Billy realizes that any hopes of this being a mistake are dashed as he notices heavily armored machine guards called Boxbots awaiting them. As the mutants huddle together out in the cold Billy understands that this is now their home. Once others start realizing it too, things begin to get ugly. Two of the mutants, Diamond Lil and Random, decide they have had enough and challenge the authority of the Boxbots. The robots reply swiftly and brutally as they unmercifully pound their opposition. Maggott and Billy’s father want to do what any hero would do in this situation but a nearby voice warns them otherwise. The voice belongs to Dr. Cecilia Reyes, one time X-Man and a former teammate of Maggott's. She informs them that any confrontation with the Boxbots would be purely suicidal, especially since they are powerless. As the Boxbots continue to pummel the two unruly mutants, the Taylor family and Maggott try using their powers to confirm Cecilia's assessment and realize that they are indeed powerless. Cecilia points upwards and remarks that the culprit is a boy about Billy's age whose power is the ability to cancel out the powers of other mutants. They look atop a guarded tower to see the boy named Leech restrained to a satellite like device as his powers are broadcast over the compound.
Mr. Taylor says it is hypocritical since their captors obviously don't mind using mutants for their own benefit. As the Boxbots begin to round all the mutants up and lead them into the building they realize that they are running out of options. The mutants are led into a room in which they find a scientist sitting at a desk. It is a simple setup in which they are being questioned about everything form what their powers are to who their school teachers were. Billy’s father refuses to cooperate, insisting that he has rights. The scientist takes Mr. Taylor‘s outburst rather well and then Billy notices that on the wall behind the desk is a broken man whose mutant power is being a mind reader – they don’t need his father’s cooperation.
After interrogation, the mutants all find themselves divided into two groups. Billy and his family are part of one group which is distinguishable by the green M's on their hand. However, Maggott belongs to the other group which has red M's instead. As they try to determine what the different colors mean, Maggott believes he knows the answer. He states that one of the groups wasn't going to make it out alive. Maggott figures since he never has any luck at these sort of things he needed to do something about it. Maggott kneels down between the two kids and asks them to take care of one of his slugs for him. By doing so at least a part of him would live on. Cecilia insists that Maggott is overreacting to the situation because this isn't Nazi Germany it is modern day America. However, Maggott doesn't answer her because he somehow knows that he is right. Finally Wendy agrees to take one of Maggott's slugs.
Right then the Boxbots begin to round up one of the groups and it happens to be the group that Maggott is a part of. The Boxbots wield their energy rods and lead all of the red M'd mutants into a different part of camp. Billy can't shake the feeling that Maggott just might be right. He has to know the truth so he sneaks off behind the watch of the Boxbots while he hopes that Cecilia was right and Maggott was simply overreacting. Billy can barely see anything as he peeks through the windows of the building that the group was led into, but he manages to hear a voice which belongs to the man standing next to Maggott. The man asks Maggott what he is doing in which he replies praying. Billy continues to watch through the window. His eyes begin to widen and his hand covers his mouth as his eyes change from curiosity to horror. He realizes that Maggott was right in his assessment of what would happen. Billy watches in horror as tears roll down his face.
(the next day)
The inmates of the camp are all lined up for assembly, and they are introduced to someone called the Director. Just by the way the other agents acted around him was without a doubt certainty that the Director was the man in charge. Billy thinks of how disgusting the Directors face is. The rumor around the camp was that a mutant was responsible for his disfigurement. Billy doesn't believe that there was a single word of truth that came out of the Directors speech. In fact, Billy almost threw up when the Director promised that once everything got under control those who were innocent would be free to go. Suddenly Mr. Taylor interrupts the Director and questions him about the red M's. Billy had told his father everything that he had saw the night before, so when the Director lied about them simply being in some different camp, Mr. Taylor calls the Director on it as his wife tries to stop him. Billy‘s father confronts the Director on the set up he is running and how the camp really serves as a weeding out process in which the agency keeps any mutants they deem valuable and kill the rest. The Director laughs as he pushes Mr. Taylor against the wall and saying that he has a vivid imagination. The Director suggests that they go somewhere a bit more private. Two Boxbots escort Dad out and that is the last time Billy ever sees his father.
Those fortunate enough to be still alive do what they can to stay that way. The living conditions are extremely poor and people are sick, with little in they way of water, food, and medicine. Cecilia desperately does whatever she can to help the sick and Billy chips in any way he can too. They both know that their efforts are only part of a losing battle because as long as the “sessions“ carried on, people would only get weaker, ill, and continue to die. Billy's mother is currently in a such a session during which the agency attempts to extract whatever powers they can from the mutant detainees. Kane carries Billy's mother back to the barracks, accompanied by Dr. Windsor and a Boxbot. She describes the process as what an orange must feel like after a juicing. But this is all old news compared to the offer they just receive from the Director's right hand men.
(over the next days)
Kane and Windsor say that for those who give themselves over to the program not only the sessions will stop, but they will also get out of the camp. Two of the mutants, Wildside and Reaper, are the first to accept their offer though in the following days more accepted. Although Billy doesn't like the sound of the so called program he feels that they should at least take it into consideration because mom is in a very bad condition. However she tells him that she would rather die than become a slave for these people. Plus, she has found another way. Dr. Windsor, of all people, is secretly helping people escape and she made "arrangements" for Billy and Wendy to go next. Even though it is a big risk Billy is ecstatic at the possibility of going home. The one thing that bothers Billy is that while his mother mentions Billy and Wendy in her plans she makes no such mention of herself. Dr. Windsor informs them that unfortunately he can only take two people at the moment. Billy starts to cry at the thought of leaving his mother behind in this nightmare, but tells him to be a big man and buck up for Wendy's sake. She smiles as she wipes the tears away from Billy's face and assures him that she will be following soon enough. Billy concedes and hugs his mother knowing that it is the last time he would ever see her.
Dr. Windsor is true to his word and comes the next night for Billy and Wendy. As he walks them hand in hand Billy reflects that he doesn't ever recall being so nervous in his life. Yet despite the freezing cold of the compound, little beads of sweat are forming on his forehead as Dr. Windsor delivers the guards his cover story. The guard sarcastically asks Dr. Windsor if he is taking the kids for a special experimentation before allowing them to pass through the gates. Billy can't believe how easy it was for them to escape. He turns to take one last look at the camp and like Maggott before him, says a prayer. As Dr. Windsor leads Billy and Wendy out of the camp, Billy prays for his parents and everything that he has lost. He prays for the uncertain future that lies ahead for Wendy and himself. But most of all he prays that someday soon the monsters would go away.