Attached to a complex machine, Professor Charles Xavier is assimilating information from all around the world, using his incredible brain to process the huge amounts of raw data in an astonishingly short amount of time. It is easy for people not in the know to underestimate him as his main talents cannot be shared with the rest of the world. The machine is in his ready room, several hundred meters below the mansion, where he has been for some time now, watching television news reports, bringing up computer files and cross-referencing everything he gleans from these sources; some of which aren’t exactly legally obtained. Unfortunately, all of this information means that the Professor may well be the lone witness to what may very well be the first day of the end of the world.
Someone buzzes at his door and the Professor asks them to enter, if they must. Bishop walks into the darkened room behind Charles and asks him to pardon the intrusion, but it has been seventy-three hours since he sequestered himself. Charles replies that, no doubt, Jean asked him to check in on him but he is perfectly capable of looking after himself. Bishops says that he doesn’t doubt that, none of them do, but he was actually hoping to discuss something of a more personal nature. Charles glances round at Bishop, apologizes for being egocentric and asks him to continue.
Bishop tells him that, while it shames him to admit it, it is obvious to all parties concerned that admitting him to the X-Men was premature at best. In the future where he was raised, his ‘direct approach’ was more than acceptable; indeed, it was absolutely necessary. Clearly, that is not the case in the here and now and, rather than continue as a disruptive influence, he regretfully tenders his resignation. Charles removes the helmet he was wearing and replies that, at the risk of sounding insensitive, “Poppycock!” He tells Bishop that, though it may sometimes seem the contrary, attending Xavier’s is as much about learning as it is fighting. If Bishop fails, then he fails and that’s not going to happen. Bishop has never struck him as one to give up easily and, therefore, his resignation is not accepted. Bishops understands and even gives a little smile, as Charles asks him to have Ororo bring the van round out front in five minutes. “Done and, Professor, thank you,” he replies as he departs.
Sixty miles away up the Hudson River in Middleborough, sits another school of an entirely different kind. However, Our Mother of the Sacred Heart and Xavier’s do share a member of staff: Sharon Friedlander. Dressed in a long, white lab coat, she folds some sheets and thinks it’s funny that yesterday she treated three runny noses, two scraped knees and a black eye; a bit pedestrian compared to her responsibilities back when she watched over the New Mutants. Mind you, here she doesn’t have to worry about having her molecular structure rearranged in the whim of one mad mutant or the next. She has no regrets over her tenure with the Professor, or she’d have never accepted this latest babysitting assignment. Suddenly, a fist comes through the curtains next to her and smashes her in the face, breaking her neck. Several Acolytes then appear, standing over her. One asks Cargill if that was really necessary and she replies no, but it was fun.
Back at Xavier’s, Jean Grey is holding a Danger Room session with Archangel, Bishop and Gambit. She asks Bishop and Remy to lose their weapons and informs them that the object of the lesson is for them to touch her without using their mutant powers. “Don’t need no Danger Room for dat, chere,” replies Remy, “All you gotta do is ask. So what’s the catch?” Archangel suddenly takes to the air and the Shi’ar technology which the Danger Room uses creates holograms of him so they don’t know which one is real. He is Jean’s back up. Remy turns to Bishop and asks him if he realizes that this is a thinly veiled attempt at forcing the pair of them to make nice. Bishop responds by asking if he questions his professionalism, which Remy does. Bishop tells Remy that he may not like him any more than he trusts him, but Remy is an X-Man nonetheless and, as such, he will defend him as if he wasn’t the homicidal traitor to the cause he suspects him to be.
The lesson begins and Archangel fires a cluster of flechettes from his metallic wings at them and they dive in opposite directions, away from the danger area. Gambit tells Bishop that, for a body whose references and prior work history is some hundred years in the future, he’s a fine one to question another body’s loyalty.
In Central Park, New York City, Detective Charlotte Jones is out jogging. She’s been working out of Manhattan homicide for two months now and it still seems a little unreal. She’s worked hard; raising little Timmy during the day and working nights, studying for her exams every free minute in-between. The big question she asks herself is: why is she risking everything she’s strived for to help a group of outlaw mutants? She slows to walking pace and approaches Professor Xavier and Storm, who are waiting for her. He thanks her for meeting them at such short notice and trusts she brought the information that he requested. She pulls a document out of her pants and tells him that the coroner’s report is right here and is his, quid pro quo. She asks how she knows that she’s doing this of her own free will and he isn’t using his mental powers on her. Storm is about to argue for Charles but he cuts in, replying that it is a perfectly reasonable question and the honest answer is, she’ll just have to trust him.
Suddenly, Charles receives a distress call from Sharon Friedlander, a final act of desperation just as she is punched by Joanna Cargill. This is serious. Back in the Danger Room, Jean prompts Warren as Bishop and Gambit are getting a little too close for her liking but, before they can tag her, they are struck down by a powerful telepathic call from the Professor. Bishop wonders if it’s another hologram but Gambit replies that it isn’t, unless a hologram can go shouting inside a person’s head. He tells them that he has no time to explain, but they must report to the hangar, immediately! They must go sixty miles due north and he will elaborate on the way there. There isn’t a moment to lose as one innocent may have already lost their life and dozens more hang in the balance.
A yellow school bus approaches Our Mother of the Sacred Heart. The children aboard are singing merrily; “The wheels on the bus go round and round.” The driver, Tom Corsi, thinks it is rather odd that Sister Ignazio isn’t waiting out front to greet the kids. Class starts as soon as he lets them off and he wonders why the school looks like a morgue. The Acolytes watch through one of the windows, as the bus moves closer to the entrance and then stops. Young Teddy Matson asks Tom if he’s letting them off but he replies that he isn’t and puts the bus into reverse gear, edging slowly away from the entrance. He feels something is wrong, that they’re being set up. He doesn’t want the kids to catch on but he needn’t have worried, as a massive explosion blows apart the school building in front of the bus, shattering the windows.
As the smoke clears, the costumed forms of Carmella Unuscione, Joanna Cargill and the three Kleinstock brothers can be seen, with Cargill holding the limp body of Sharon Friedlander by the hair. Unuscione’s exo-skeleton crackles around her. The Kleinstock’s were responsible for the explosion and she tells them that, if they’ve jeopardized the mission with their reckless behavior, they will answer to no less than Cortez himself. Their hands glow with power, as Cargill reminds Unuscione that securing the ‘unidentified mutant‘ is only part of the inquest. There is also the cleansing of young humans from the gene-pool, such is their right, their responsibility as Acolytes; as Magneto’s chosen.
Erik Kleinstock takes to the air and heads towards the wrecked bus. He says there is nothing in Magneto’s readings that says they cannot enjoy their victories. For decades, mutants have been hunted, enslaved and, all too often, executed and he's all too happy to return the favor. Unuscione orders him to stand down until the area is secure but he turns and tells her that she’s being overly cautious. They know the homo superior on the bus is still in his latency phase and she surely isn’t frightened by these filthy flatscans? Suddenly, a gunshot comes screaming through the windscreen and goes straight through Eric’s body, killing him instantly.
Tom Corsi leaps from the bus through the window, taking the action away from the children he is entrusted with. He berates them for their use of racist and derogatory language as he continues firing, thinking that his ten years as a cop wasn’t a total waste. Unuscione grabs him in her exo-skeleton and lifts him high into the air. He manages to joke, despite being helpless in her grasp. She tells him that he has slain a fellow Acolyte and that will cost him his life. He says that she should have mentioned that earlier; he would have settled for giving him a flesh wound. She wonders why he is remaining so calm in the face of certain death but then receives her answer. Energy blasts hit the ground all around them and they lookup to see the four X-Men arrive on the scene, Bishop armed with a gun and Remy throwing kinetically charged cards towards them. Jean says that she hoped that the Acolytes had disbanded after Magneto’s death but that obviously isn’t the case.
Gambit tells Bishop, “Y’know how Storm’s always sayin’ dere are times you should mellow out, rein yourself in? This is not one of those times.” Cargill charges them both, saying that, if they were true mutants, they would follow the teachings of Magnus, fighting at their side to purge the world of the genetically impure. As she grabs them, Jean recognizes her as being Frenzy, who she faced back in her X-Factor days. Charles had wondered where the Acolytes were recruiting new members from. With her concentration broken, Unuscione takes the opportunity to grab her with her exo-skeleton, while the two remaining Kleinstock brothers, Harlan and Sven, both fire their plasma blasts at Archangel, who crashes to the ground in a ball of flame. Jean hopes that following Apocalypse’s experiments on him, Warren can survive the attack.
Infuriated, she takes to the air and one of the Kleinstock’s tells her that she has seen how easily her comrade has fallen. There is still a chance to save herself and change her allegiance. If she is not with them, she is against them. She replies that she is most definitely against them. She manages to discorporate Unuscione’s exo-skeleton and slams the brothers together with her telekinetic power. She says that the Magneto she knew may have been determined, even brutal but he would never strike out at innocent children. To her amazement, the brothers begin to merge together, their bodies morphing, increasing their size. They call her a blasphemer. Magnus was a great man; one who wasn’t afraid of making difficult decisions. How dare she sully his name by painting him a coward? He died for their sins so that mutants will inherit the Earth. Bishop tells them that he has seen the future and they’re not in it.
Jean telepathically asks Bishop if he can handle their plasma blast and he replies that they shall find out. Gambit, meanwhile, runs from Cargill, who chases him, asking if this is what it means to be an X-Man; to run away? Remy tells her that people change and he never took her to be a mindless sheep. He runs underneath a frame with a tire attached to a rope hanging from it. As he pushes it away from him, he charges it and, as Cargill follows him, the tire comes around and hits her from behind, exploding upon impact.
Unuscione realizes that the X-Men are far more worthy opponents than Cortez has led them to believe, which is all the more reason they must increase their numbers for the sacred wars to come. She uses her exo-skeleton to reach inside the bus, through a tear in the side, saying she can use her power to divine the chosen, so that they might be raised among their own people, instead of wallowing amidst this human sty. She picks up Teddy Matson and brings him toward her. “What is this?” she asks, as she gets a good look at him, “Xavier has played us for fools. This child is obviously flawed by human standards; there is no place for imperfection in their new order.”
Archangel then breaks free from the ground, having survived the Kleinstock’s attack. He asks if this is how they honor Magneto’s memory. His entire family was wiped out by people who felt like they do; supremacists who believed they had a right to decide who lived and died. He tells her that the child has Downs Syndrome and has as much right to live in anyone’s order as she. There’s nothing new about ignorance, intolerance and hating what you don’t understand. So long as there are people like them, there’ll be people like the X-Men who’ll be there to stop them.
She deposits Teddy, saying that is nonsense. The child is as useless to Xavier as he is to the Acolytes. He belongs with the rest of this human kindling and tells the Kleinstock’s to ‘purify’ them. Bishop leaps at them, warning them that, if they do, he swears by all that’s holy that he’ll hunt them down and make them pay in kind a thousand fold. He manages to get in a right cross as they fire and the blast goes wide of its target, igniting the bus, which means that his intended victims will only die that much slower. Gambit uses his cards to create a wall of energy between the flames and the children, as Archangel swoops down and begins collecting them. One of the boys, Dwayne, says to Warren that he’s an angel, asking if they died in the explosion. Teddy tells him he’s a jerk; the guy’s trying to save them.
Jean smells gas and Bishop tells the little ones to keep moving away from the bus. Out of nowhere, Storm appears in a clap of thunder which signals her arrival. She summons fire-dampening rains to quell the flames, as she gracefully descends to the ground, asking what monsters are they that they threaten the lives of children, no matter what the cause. Gambit looks around, replying that they are monsters who have escaped. At least they saved the children. Storm asks if they really did, or have they just sentenced them to a world where no man is safe from his brother. He says that if they were fighting on their own, definitely, but that isn’t the case, not by half.
Later that night, Charles Xavier watches a new report given by Trish Tilby, reporting on the incident. She tells her viewers that an estimated fourteen school employees may have died when the building exploded. Authorities are withholding names until families have been notified. She adds that, while noone is willing to officially exonerate the X-Men, witnesses confirm that they were defending the students from a fanatical band of genetic supremacists known as the Acolytes. She hands over to Senator Robert Kelly, chairman of the committee on mutant affairs who has toured the devastated area.
Senator Kelly looks at the camera and tells the viewers that he wishes that he could say he was shocked by what he’s seen here but, the truth is, he’s spent the past ten years of his life predicting such an incident. He says there are people in the government and the liberal media who, for whatever reason, would like everyone to believe that they have nothing to fear from the mutant populace. He urges the American public to wake up and see the ‘mutant menace’ for what it is; if for no other reason than for the children. Charles uses his remote control to switch off the television, contemplating yet another setback in his dream of coexistence.