The past…a world in which more people have died in the name of religion than of cancer. Crucifixions; warfare; missionaries; concentration camps. What is it that makes people who believe in one god so angry with those who believe in another? What is it that makes the teachings of respective deities that makes someone more right – or wrong - than the next person? What is it that makes people go to holy war against those who pray to the same god with different words?
Do not follow other gods, any of the gods of the peoples who are all around you, because the Lord your God, who is present with you, is a jealous God. The anger of the Lord your God would be kindled against you and he would destroy you from the face of the earth. – Deuteronomy 7:14
The present…The Xavier Institute for Higher Learning. Out the front of this school, where those who are different are taught not to fear those who are "normal." Six crosses stand upright, each with a mutant crucified upon it. Several of them wear the X upon their clothing. There are others who also wear the X. They stand in shock at the horror before them, who is capable of doing such things? And at their home too? Wolverine; Phoenix; Cyclops; Iceman; Nightcrawler; Husk and Chamber, all are or were X-Men, and none are prepared for the events that are to follow.
Jean tells the others that she cannot feel any thoughts from those on the crosses, or pick up any heartbeats, and announces they are all dead. Wolverine tells his teammates they should get them all down from the crosses, while his good friend Nightcrawler suggests they don’t, for fear of disturbing the forensic evidence. Cyclops, for a change, agrees with Logan and repeats his words, but Iceman tends to agree with Kurt and is about to say something about the police before the leader of the X-Men, Cyclops, shouts out for them to be taken down. Kurt and Bobby still look a little wary, but comply with Scott.
Cyclops tells Jean to contact Annie, the school nurse and to get her to come out here, Jean replies to her husband the same way she has been a lot as of recently, very nonchalantly, but does as he says and telepathically contacts Annie Ghazikhanian. She asks Annie to stop screaming, as it is only telepathy and it is not going to hurt her. Not too impressed with Annie, Jean tells her to join them out front of the school when she pulls herself together as they need her help quickly.
Nightcrawler is helping Wolverine take down former X-Force member Jesse Aaronson, and tells him that the police are going to be unhappy they tampered with the crime scene. Wolverine tells Kurt that despite the fact he never does, he agrees with Cyclops, and when it comes to mutants, the X-Men are the police.
Meanwhile, Husk has spotted someone who she knows, and tells Chamber that it looks like Jubilee. Wolverine overhears and leaving Kurt runs over to where Iceman is, who tells Logan that it is Jubilee. Logan raises his voice at seeing his close friend in this state and shouts at Bobby to get her down. Bobby tells Logan to calm down as he is trying. Logan tells him otherwise, and raises his voice again, calling for a healer – Xorn or Archangel. Carrying Jubilee in his arms, Logan rushes to the mansion. Meanwhile, Husk has spotted another of her former Generation X teammates crucified – Skin.
Nightcrawler is pulling someone off a cross and says a prayer – "Oh Lord, how long shall I cry for help and you will not listen? Or cry to you "violence" and you will not save?"
The X-Men carry the bodies into the mansion where they meet up with Annie. She asks Iceman who did this to them, and how anyone could do such a cruel thing. Bobby gives Annie a nasty look fraught with meaning and tells her that those who did it are people who don’t like mutants – he doesn’t need to add "like her." Jean and Kurt look at Bobby, carefully watching whether or not he will go any further in the conversation, though he says nothing else.
In the infirmary, Archangel lays upon a bed in the center of the room, ready for his healingblood to be drained in the hopes of reviving the dead mutants. Wolverine stands at Jubilee’s side, Husk at Warren’s and the other X-Men mill around Annie who reminds everyone that she is just a nurse, and that they need to get a doctor at the mansion too. Wolverine raises his voice and asks Annie how long it is going to take, while Warren tells him to be patient and calm down. Paige asks Warren if he is sure he is up for what is about to take place, and he tells her he is, and that she should be more concerned with Jubilee and Skin.
Phoenix tells everyone that she cannot reach Xorn telepathically, but is trying for the Professor again.
Meanwhile, Cyclops takes Nightcrawler aside, telling him he wants a word with him. He tells Kurt that he wants him to get his squad together in the conference room – Kurt cuts in and tells Scott that it is not just his team anymore – before Scott cuts back in and tells him that is his team, and reminds him that he wanted more responsibility, and so Xavier gave him the second squad. Cyclops folds his arms and tells Kurt that whether he chooses to follow up on the responsibility given him, is his business, but he is team leader.
Nightcrawler smiles and tells Cyclops that as team leader he found it easier to share responsibility with Archangel.
Cyclops gets stern with Kurt and tells Kurt that what really happened is that he found it easier to be liked if he did not have to make the unpopular decisions, and left those decisions to Warren so that he could continue to be everybody’s happy-go-lucky best friend.
Nightcrawler seems quite offended by that and tries to say something, but Scott continues talking: he tells Kurt that being a leader is not about being a friend or being liked, but about making the right decisions no matter how hard they are to make, or how unpopular they make you. As Cyclops walks away from Kurt he tells him to get his team in the conference room, and to do it now.
Nightcrawler approaches Logan and says to him that he heard Cyclops, as in implying to get to the room. Wolverine just tells Nightcrawler that he hears too much of Cyclops. Annie reports that they have so far taken almost a pint of Warren’s blood, and he tells her to keep going. Paige, concerned for his safety, protests, and tells Annie that she has to stop at some point. Warren tells Husk that his new healing powers will keep him going, to which she tells him that he does not know that. Nightcrawler reminds Paige that they have to meet with Scott’s team, but Husk just tells him that she is staying.
Warren looks up at her from the bed and tells her that she, and Chamber, should go with Kurt as she is just wasting her time here anyway. Paige is shocked and taken aback. She turns and walks away and angrily tells Jono to come with her.
Annie, at Warren’s side, tells him that what he just did was not very nice, and adds that Paige talks about him all the time, that she cannot get her to shut up sometimes. Warren tells Annie that he knows – but that Paige loves Chamber. Annie looks shocked and asks him if he is talking about ‘the kid without a mouth and tells Warren that there is nothing there to kiss. She tells Warren that if he knew anything about women he should know there is nothing more important than a man who can kiss…all of which Chamber overhears as he leaves the room.
In the war room, Cyclops stands in front of several of the X-Men, most of them from Kurt’s squad, and asks them who is behind the slaughter. He tells them he wants hints, rumors, clues, and psychic impressions - whatever they have got, and they will find the monsters that did it. Havok, in his new costume, stands up and tells his brother that with the crosses and religious symbology, the idiots in the priest costumes he and Kurt ran into a few weeks ago are a good bet.
Kurt agrees with Alex, and tells everyone they are called the Church of Humanity. Cyclops coldly asks him who the Church of Humanity are.
Kurt senses the anger in Cyclops voice, and hesitates before tells Scott an the others that the Church of Humanity are a group who think mutantkind is against God, and that his team have faced them to varying degrees recently. Cyclops gets madder and barrages Kurt with questions like their background, locations, how many times his team has faced them and why wasn’t his team informed on them. Kurt again hesitates, and tells Scott that he thought his team shut them down in Montana, but they kept reappearing, and he thought Warren would have briefed him on them. Cyclops raises his voice further and asks Kurt if he is brain-dead, and whether he did or did not ask Xavier for more responsibility at the school.Everyone in the room, including Kurt goes very quiet, some obviously uncomfortable by Cyclops harsh tone of voice and words.
Cyclops asks Nightcrawler if Xavier gave him the second squad as per his own request. Nightcrawler frowns and tells Scott that Xavier did. Scott tells Kurt that that makes it his responsibility to inform the other teams of potential threats to mutantkind, especially if his own team has failed to deal with them effectively. Iceman begins to protest, and Havok backs him up, telling his brother that he seems to be doing a lot of "Monday morning quarterbacking" at the moment. Scott tells his brother, with all due respect, that this situation does not concern him. With all due respect back, Alex replies, this is no time to be a tightwad, and as a mutant, it does concern him.
Alex tells his older brother that he is siphoning off all his anger through authority again, and right now what they need is a more positive, pro-active approach, they need to get moving before someone else dies.
Meanwhile, back in the infirmary, Warren says that he is a little light-headed, Annie tells him that they cannot take any more blood from him, and that as the machines are all blank, she does not think it is working. Annie asks Logan if he is seeing anything she misses. He tells her ‘no’ that Jubilee, and looks to the others – Magma, Skin, Jesse Aaronson and the other two are all the same. He tells Annie to cut Warren from the transfusion, which she does, to Warren’s feeble protests, telling her to wait a little longer. Annie tells him she cannot, as his healing ‘thingie’ is not replacing his blood as fast as she drains it. Wolverine tells Warren not to make him come over there, and tells Annie to cut him, as they do not need any more dead today.
Suddenly a very faint ‘Who died?’ is heard. Annie turns around in shock, and Warren asks if that was Jubilee? Logan brings his face up close to that of Jubilee’s, and smiling, pleased that she is alive, tells her that she died, and it scared the life out of him. ‘Cool’ she says before asking Logan if he has heard of the words "mouth wash."
Back in the war room, Cyclops asks Nightcrawler if what he has just told him is that the previous time he encountered the Church of Humanity they said they had to leave him alive, but then the next time they were shooting at him. Kurt tells him that he right. Scott asks Kurt what changed between then and now, meaning specifically with him. Nightcrawler says that the only major thing is that he renounced his priesthood.
Odd looks begin to fly across the room and Havok asks him if he was joking when he just said he was a priest. Very seriously, Kurt tells him he has been studying to be a priest for years now, and was recently fully ordained. He asks Alex why he finds that so hard to believe.
Havok says ‘no offense’, but tells Kurt to look at himself, and asks him how it would work, and if he is talking about being a priest to mutants. Iceman interrupts and asks Kurt if he just said he made the priesthood, and if there was a ceremony, why they were not invited to it. Kurt looks around at his friends and teammates and tells them they were all there. Havok and Iceman both look concerned for their friend, while Phoenix appears as if she is trying to read him. Polaris has her chin resting on her hand and looks very unimpressed with the whole situation, while Husk and Chamber look awkward. By the expressions on everyone’s faces, Kurt goes wide-eyed and a little scared, asking them all if they were at the ceremony. Cyclops looks angry, and asks him where the "ceremony" took place.
Back in the infirmary, Annie is tending to the only other mutant that they managed to save thanks to Warren’s healing powers, the former New Mutant known as Magma. Alex, Kurt, Paige and Jono, enter the room, Kurt tells Logan that they need him, and upon seeing Jubilee alive, Husk rushes over to her, and the two friends hug and Jubilee says ‘Trust that old Guthrie enthusiasm’, before starting to cry. Husk asks her what the matter is, and Jubilee looks over at their former teammate Skin. Husk cries out and comforts Jubilee, who was close to him, as she mourns at his side.
Shortly after, outside St. Michael’s Church in Brooklyn, Wolverine, Cyclops, Phoenix, Havok, Polaris, Iceman and of course Nightcrawler are preparing to enter the church.
Alex asks Kurt what the Church of Humanity could have possibly hoped to gain by convincing him that he had become a priest. Kurt says he doesn’t know, and asks that everyone stop asking him that question. Cyclops tells everyone the church looks like it was abandoned a long time ago, and asks Kurt if it is the same church he always went to.
Nightcrawler tells him that it is, and that when he was doing his priestly duties – or at least what he thought were his priestly duties, he was under the observance of a man named Father Whitney, and the church was always well-maintained. He says that the ordination ceremony he remembers took place inside the church.
Everybody looks at Kurt a little strangely still, and Wolverine tells him that they were all never here. Jean adds that there is some psychic residue of someone tampering with his mind.
As Kurt walks up the steps to the church he tells Phoenix that in a way he is almost glad to hear her say that, and adds that he had begun to doubt Father Whitney despite his warmth and friendship recently, and tells everyone that it is funny how kindness often turns out to be more than just a pleasant act of selfishness.
As Kurt unlocks the door to the church with his key, Cyclops tells Wolverine to wait out front and cover them, while Polaris to go around the back and come in from that way. The door creaks open and the five X-Men enter the church and as Cyclops points out, the church, which has been empty for a very long time.
A rat scurries past the super heroes along a pew and Kurt tells them all he knows he was here, and reminds them that people saw him leave the mansion, that he never made a secret of the fact he was training to be a priest.
Alex asks him how he could be a priest yet again, as he looks like a devil in the house of God. Kurt tells Havok that he used one of his old image inducers to make himself appear human. He digresses that in retrospect it goes against everything he believes in…Alex tells Kurt to imagine what would happen if the inducer failed during a mass, and quotes a passage from Revelation: "and the devil who had deceived them was thrown into the lake of fire and sulphur, where the beast and the false prophet were, and they will be tormented day and night forever and ever".
Kurt looks surprised, but somewhat impressed, that Alex knows scripture by heart, and Alex tells Kurt that he knows Revelations, though it was more like science fiction to him when he was a kid, and tells him that he was raised a Roman-Catholic by the family that adopted him. Cyclops asks Kurt if there are any other rooms in the church, and he replies that there are some small alcoves and Father Whitney’s office out the back.
Jean notes some blood on the floor, and can tell that it is mutant blood, and that there are trails of it leading out the door from the back room. Someone asks how she can tell it is mutant blood, and Jean smiles, and tells them that she can tell a lot of things about the place that no one is going to like.
She asks everyone to stand back, before she telekinetically rips the floorboards up. And the five X-Men stare in shock at the horror beneath the church floor…some kind of laboratory, where mutant bodies, some dead, some dying, others in pain, lay all over the floor, strapped to tables, tied to equipment an suspended in tanks, while the blood flows towards a drain in the center of the room…next to a withered man in a wheel chair who glares at the X-Men, and who may hold the answers the X-Men need!