St. Michael’s church, Brooklyn, where after six mutants were crucified on the X-Men’s front lawn, Wolverine, Cyclops, Phoenix, Havok, Polaris, Iceman and Nightcrawler have gone in search of those who committed the terrible act – the Church of Humanity. Now, the seven mutants stand by the broken floor which Jean Grey ripped up, to reveal beneath it dozens of mutants, all dead, dying or otherwise. And the X-Men are speechless.
Nightcrawler ties directly into this, and thinks to himself that through Genesis 28, the word of God gives mankind the right of domination over all beasts of Earth, that once a people is "demonized", equated with something less than even human, that by the word of God, mankind has dominion over them.
Alex Summers tells Kurt Wagner that he knows what he is thinking, and trying to reassure him tells him that this horror has nothing to do with him. Nightcrawler doesn’t look at Havok and just says ‘Oh really?’
In the laboratory below, one of the figures lying on the ground stirs – it is Father Whitney. The wounded priest sees Kurt and raises his hand. Kurt thinks about how the same people who believe they have dominion over others believe that by aborting a fetus that you are murdering human life, and that human life is sacred. Kurt Wagner sees Father Whitney and teleports down below to get him, all the while thinking about the fetus and that until it is born and old enough to become a soldier for another country – evil, or collateral damage.
Cyclops asks his wife if there is still anyone else alive down below. Jean tells him there are a few, but they won’t be alive for long.
Kurt has reached Father Whitney who tells Kurt that he is sorry. Scott asks Phoenix if she can telekinetically remove the mutants who are still alive, and in answer to such a stupid question Jean just says ‘Of course’ and asks everyone to make some room – as she doesn’t want to catch any of the mutants on the jagged floor. The most powerful telekinetic in existence lifts a dozen or so mutants, and Nightcrawler and Father Whitney up to the church floor.
Kurt kneels over, holding Father Whitney in his arms, and the priest tells Kurt that he was right to question him, and to realize that wearing a collar and living in a church does not make you closer to God. Father Whitney speaks slowly, the remains of his life hanging on to finish what he must tell Kurt. He tells him that they were so angry with him when he failed to keep him in the priesthood, that he couldn’t curb his lustful desires. Father Whitney continues, saying that he spent much time convincing them that Nightcrawler would be their greatest achievement – their key to the world…once he became Pope. Kurt looks shocked, and asks Whitney what he is talking about.
The Father doesn’t answer him and continues with the story, about how he tried to find another to replace him, so many, as he can see by the mutants in the church. The Father’s time is growing closer and he cannot finish telling Kurt something about himself, but tells him that they are in Montana – that they never left. Father Whitney begins to cry, and apologizes to Kurt, telling him he was just doing what they told him, and that he never expected to like him. Kurt asks Father Whitney if it is the Church of Humanity that is in Montana still and what he means by "They never left." Father Whitney says ‘I never expected to grow fond of a mutie…’ and passes away, tears still in his eyes.
Kurt looks at the man he once admired and says nothing for some time. He stands up and takes command of the situation. He tells Cyclops to get in touch with the Xavier Institute and the local hospital, and to get Archangel and Xorn, their healers, here now, and that when everything is in more capable hands than theirs, they will leave for Montana.
Later that day, the X-Men are in the X-Jet, headed for Montana. Inside, Nightcrawler tells Jean and the others who weren’t there last time when they fought the Church of Humanity what happened. He says that they got to their compound outside of Butte, knocked them around a bit, but came away with nothing. Jean guesses they all teleported out when things turned bad, and she tells everyone that based on what Father Whitney said, as well as the mind tampering Kurt has obviously been through, Jean thinks that the Church of Humanity never left Montana, and that Kurt and the other X-Men were just made to believe they did.
In one of the seats towards the back of the plane, Havok tries to make sense of what happened and says ‘A mutant-hating, gun-wielding, mind-controlling religious sect in the middle of Montana turned you into a priest. Sounds reasonable – but then I hang around with people who read minds, have claws, teleport, control magnetic fields and shot power beams out of their eyes…so I’m hardly grounded now, am I?’ Wolverine smiles and sarcastically asks Alex if he thinks there is something unusual about the X-Men.
Phoenix tells everyone that she will scan ahead to see if she can pick up a psychic signature strong enough to mind-control on the level she is presuming, and Nightcrawler tells her he has no doubt she will find one. As Jean starts to scan, she warns everyone that this may alert the Church of Humanity to their presence. Kurt just says ‘Good.’
Inside the cathedral in Montana, Hidden beneath his hood, someone says to the leader of the Church that he can actually see the X-Men projected into his mind by Mutant 143, and comments that Mutant 143 must have been very effective in convincing Kurt Wagner into believing he was a priest. The figure dressed in red, the leader, asks if ‘the demon’ is with them. The other person says that he is, and seems to be leading the X-Men. The Pope says that it is good, especially as Wagner is such a terrible leader, and says that is why he was ultimately wrong for their plans, and that it is just unfortunate how they were blinded by Kurt’s love of God, and the ability to hide his true Satanic appearance under a human face with the image inducer.
The red-dressed figure tells the other that it would have been perfect to place the demon-faced mutant as the successor to the current Pope allow Wagner to "take his seat in the temple of God’ as it says in Thessalonians, only to be revealed by an aptly timed failure in the image inducer, as „Satan". "Who uses all power and every kind of wicked deception", leaving the church forever destroyed. The figure hidden in the shadows continues the leaders plans, and says that mutantkind would have been hunted down as deliverers of the Antichrist, and the western world would have been lost – with only them to turn to for spiritual solace.
The shadow-hidden figure says it was a complex, but potentially powerful plan, ruined because Kurt Wagner, like all young men, could not control his sexual urges and remain a priest. The red figure now turns to the two men who have been put to their knees before him during this conversation, and reminds them it was their mission to end Father Whitney’s failed experiment – to quietly destroy his hidden cache of potential mutant replacements for the "Wagner demon" – not to leave calling cards on the front lawn of the X-Men’s mansion in fits of religious zeal. The leader asks them if this was correct and they tell the leader that it is.
One of the soldiers says that with all the mutants Father Whitney had collected, and the plan compromised, they thought it would be the perfect opportunity to send a message. The leader puts a hand on each of the soldiers heads and after asking them why they thought it was a perfect opportunity, before reminding then that God gave them brains not to do their own bidding – the two men scream as the leader crushes their skulls, – but to do his bidding.
The Church of Humanity’s Pope tells the shadow figure – Bishop Desmond – to tell their soldiers to prepare for the arrival of the X-Men, and to use Mutant 143 to cloud the X-Men’s minds, that it will be like shooting fish in a barrel. He suggests they evacuate before the X-Men arrive as they have failed to defeat them before – the Pope interrupts and tells Desmond that before he did not want them dead – but this time he does.
The X-Jet has arrived at the cathedral, and has been shot down by soldiers of the Church of Humanity, who continue to fire at the jet. Wolverine and Polaris stand by the door hatch and Logan tells Scott, who is still inside that Kurt has teleported Jean and the others in. Logan tells Lorna that it is time for them to do their part. Lorna Dane’s eyes flash that dirty yellow color they have been turning of late and tells Logan to look at the humans below: ‘Don’t they all look like ants from up here?’
Cyclops stands by the door hatch and fires his optic blast at the soldiers while the plane nears the ground. Wolverine dives from the plane, claws out stretched and ready for action. Polaris isn’t far behind, and as she drifts to the ground, a wicked smile to match Wolverine’s rage, magnetic energy swirls and crackles around the mistress of magnetism.
On the ground, Logan guts to soldiers with his claws – payback for killing Skin. Lorna charges into battle too, and tells the humans that it would be best if they laid down their weapons – Lorna stops in her tracks, the energy dies down and her eyes return to the beautiful green they once were – she has been shot. Lorna touches her wound on her shoulder and seeing the blood says ‘I have complete magnetic control. How did these get by me?’
Wolverine is experiencing something odd also – and sniffing some of the soldiers draws a conclusion. He tells Scott and Lorna that it is all just an illusion – that they are not fighting anyone.
Optic blasts surging from his eyes, Scott starts to ask Wolverine what he means, when suddenly Cyclops gets his answer, as three bullets land in his chest.
Up on the cathedral, soldiers are shooting at the three X-Men below – all of whom are fighting imaginary soldiers. One of the soldiers says this is too easy and can’t believe that the X-Men think they are actually fighting something while they just keep getting hit with bullets. Bishop Desmond is up there too, and asks Mutant 143 if he can add olfactory sensations to the illusion, it is not too late. The wheelchair bound mutant says nothing.
Back on the ground, Cyclops and Polaris clutch their wounds, Lorna telling her future brother-in-law that she has put a magnetic shield around him. Scott ignores her and yells at Wolverine, telling him he has to get them out of here. Wolverine is charging at nothing and starts to smell something before telling Scott that he doesn’t know if he can get them out of it. Suddenly, Lorna cries out as Logan is struck down by a flame-thrower.
While inside the cathedral, a teleportation signature reveals Nightcrawler, Phoenix, Havok and Iceman have entered. Jean tells the others that those outside are being slaughtered, the X-plane has been shot down and Scott has been shot too! Kurt asks her what happened, and Jean tells him that a psychic mutant is filling their heads with illusions – she tells them Lorna has been shot and Logan is burning – Bobby Drake shows his concern for Lorna, and Alex tells Kurt he should never have let him convince him into splitting the team up. Kurt tells Alex that this is why they had to split the team up, so the others could cover them when they entered. Kurt tells Jean to go and do what she can to help the others outside now that she has covered their entrance.
Jean runs down the hallway and says that she is going after the psychic mutant. Kurt tells the others that they will get to the Pope and end the madness.
From inside a barred room, a man asks the mutants if they are the X-Men, and Kurt asks him who he is. The man tells Nightcrawler that he is a priest – a human – but on his side. He tells the X-Men that the Church of Humanity has been experimenting on him and he wants to help take them down – he tells them he knows what their plan is.
Back outside, bullets stop in mid air, and while Polaris tends to Scott, Wolverine, badly burnt, tells Lorna and Scott that he can see the soldiers up on the wall now. He starts running towards the wall, and Polaris tells him to drop and roll. Wolverine turns back to her and tells her that he won’t until he can take some of the soldiers with him. Lorna tells Logan that she is holding the bullets in place for a reason – and that he is in the way! Wolverine looks somewhat shocked, but also impressed with what Polaris has planned and he drops to the ground.
Lorna prepares for what she has to do and magnetically turns the bullets around. Cyclops pleads with her, and tells her she cant do what he thinks she is going to do – as she will kill all the soldiers! Polaris doesn’t listen to him and displays her power, sending the bullets back to where they came from – "shooting" all the Church of Humanity soldiers. Lorna smiles and in reply to what Scott said, she says ‘Yeah. I would expect so… so what’s your point? Cyclops just looks at the woman who is about to marry his brother and says nothing, but probably wonders what made the once caring Lorna turn so cold.
Up on the balcony, Desmond pushes Mutant 143 away from the carnage and back into the cathedral. He tells the mutant to begin casting an illusion that will give them time to retrieve their Pope and escape – suddenly, Mutant 143 shrieks out in pain. Bishop Desmond asks him what is wrong, and a voice from behind says ‘He tried to kill my husband – and I take that personally’. Desmond turns around and before him stands Phoenix! He pulls out a gun, points it at Jean Grey and says a prayer ‘Yea I walk through the valley of the shadow of death…protect your followers my lord, Jesus Christ…’ Jeans’ eyes flare up and she tells him that God has heard his prayer, and she unleashes the power cosmic within her, sending God’s reply – a Phoenix raptor towards him, while Desmond just screams.
Meanwhile, Kurt, Alex and Bobby are following the man they just rescued, and he is telling them that when the current Catholic Pope steps down or dies, the Church of Humanity were going to put a shape-shifter in place of his successor, which then at some point they will reveal him publicly as a mutant. The man says the mutant was going to preferably be a demonic looking mutant or someone with an image inducer. Iceman says that Kurt has some personal experience with that, and the man is surprised at meeting the one they were going to ascend to the papacy.
Kurt asks the other man if once the Church had him in place they would initiate a false Rapture- direct ascension of the "true Christians" straight to heaven to signify the "End of Days", and that when the mutant Pope was revealed by a failure in the image inducer – Alex cuts in to finish Kurt’s words – the Church is revealed to be headed by the "Antichrist" and it would be destroyed completely. Alex asks the man how they would initiate the false Rapture, and the human tells the X-Men that he has been fed a diet of holy wafers – the bread disks that represent the body of communion ritual – but they don’t taste right. Iceman asks if someone can explain all of that to the non-Catholic boy, and Alex tells him that the Rapture is the moment when God determines the world will end, and all true Christians are taken directly to Heaven, and they just vanish – right out of their clothes, jewelry, fillings wherever they are, whatever they are doing.
Bobby asks Alex if he is kidding, and what happens to everybody else. Havok tells him that they receive years of damnation, torture and hell at the hand of the Antichrist. Bobby jokes that this means Kurt, right, to which he is told that is not funny. Havok continues, saying that once the Antichrist is revealed, the true Savior arises, whom he assumes will be the Church of Humanity’s Pope. He says that they key is beginning things with the Rapture, and if they tampered with the holy wafers…suddenly the human says that the wafers were filled with something that could make Catholics all over the worl disappear – "vanish in the twinkling of an eye" he cries in pain before vanishing.
The X-Men stare at the ground where the human once stood at and suddenly, the Church of Humanity’s Pope stands before them. The Pope tells them to listen and they will hear a mystery…the Pope says they will not die but be changed in a moment – in the twinkling of an eye. The X-Men rush forward, Kurt guesses that they disintegrated the human, by activating the wafers he had eaten. Iceman says ‘Jeez, not these fools again’ and Alex tells everyone he has had enough of it all.
Havok blasts the soldiers to the right of the Pope, while Iceman freezes those to the Pope’s left. The Pope cries for the trumpet which has finally arrived, and Kurt teleports onto the Pope shoulder, grabbing the sword from the Popes hand he says ‘Woe to you scribes and Pharisees, hypocrites, for you cross the sea to make a single convert – and you make the new convert twice as much as a child of hell as yourselves’.
The Pope asks Kurt if he dares use the language of the Lord against one such as the Pope is, and tells Kurt that he may spit in the eye of the Lord, spawn of Satan who worships a godless science.
Battling soldiers, Havok quotes „the beast was given a mouth, uttering haughty and blasphemous words’. Kurt asks Alex if he is talking to him or the Pope, and Alex says to Kurt that he is not beast to him. The Pope says that none shall bow down to false idols or worship them, for their Lord is a jealous God. Kurt says ‘They worshipped the dragon for he had given his authority to the beast’ The Pope tries to crush Kurt with his hands, while Iceman is shot at by a soldier – but uses an ice blast to fight back.
On top of the Pope, Kurt says ‘You shall not take vengeance, or bear grudge against any of your people but you should love your neighbor as yourself’. The Pope smiles and says "you shall not let animals breed with a different kind" Kurt screams as the Pope tries still to crush him and Nightcrawler says ‘love your enemies, and pray for those who persecute you’…he teleports, taking the Pope’s hood with him. The Pope falls back onto some machinery, and she says "The Lord – the Lord sets the prisoners free – the Lord opens the eyes of the blind". The X-Men stare at the Pope, Kurt is shocked that she is a woman, Bobby thinks she is a cute woman, and Alex points out that the chamber is arcing, and that someone should try to save her.
Kurt teleports in and tells her to give him her hand. The Pope says ‘The Lord lifts up those who are bowed down…the Lord loves the righteous…then the righteous will shine like the sun in the kingdom of their father. Let anyone with ears listen’ The chamber with the Pope blows up – Kurt teleports out just in time, without the Pope. Phoenix and the others enter the room and join Kurt’s team. Kurt thinks that he once believed he was a priest – until he had a crisis of faith, and ruined someone’s plan for world domination.
Later, at the Xavier Institute for Higher Learning, in the days that followed, the X-Men learned that the woman who became the church of Humanity’s Pope had once been a Roman-Catholic nun. She was raped by a priest, and accused of infidelity by that priest, she was then forcibly removed from her life’s chosen work by church officials, a work she loved and did not want to leave.
Nightcrawler enters a small church where a woman is praying. And thinks that even with everything the woman had gone through, she never believed her God had abandoned her – only that he changed her life’s direction in a unique way. She never lost her faith, only in the religion claimed by his followers. A religion she felt compelled to destroy – with the help of a hated mutant. Kurt understands her perspective, even if he disagrees with her goals. Kurt kneels before the altar and thinks that everyone might have cause to fear religion at times, but he can never make himself believe that God will ever truly abandon anyone.