The X-Men track the members of the Church of Humanity to their base, where Nightcrawler is left unconscious after an encounter with their leader, the Supreme Pontiff.
In Atlanta, The X-Men confront priests of the Church of Humanity who are slaughtering researchers in a pro-mutant gene laboratory. The Church thinks the laboratory is a “house of scientific perversion” due to the place’s mutant friendly work ethic. The X-Men defeat the killers, but not before most of them teleport away, answering a summons from their cathedral. Iceman manages to freeze one of the priests before the man can escape with his brethren. Iceman suggests to the other X-Men that they should take the priest prisoner and interrogate him.
Later, the Supreme Pontiff sermonizes inside of the cathedral headquarters in Montana. The Pontiff tells his followers that they have given their lives and souls over to the Church of Humanity and “ultimate salvation.” After he expounds humanity’s entitlement to the planet, the Supreme Pontiff talks about being “touched by the universe” and becoming stronger for it. According to him, the Church of Humanity will eradicate the mutant race and maintain the livelihood and supremacy of homo sapiens.
While Wolverine takes the X-Men’s prisoner to Canada for interrogation, the rest of the X-Men stay in the Worthington Industries building of Manhattan. They examine the prisoner’s uniform and find a teleportation net and theorize that each member of the Church of Humanity must wear one, “which is either controlled by the wearer… or by remote.” Nightcrawler tells his teammates that the Church will stop at nothing to destroy mutantkind because of religious fanaticism. Stacy takes the teleportation net and Chamber warns her to be careful. Nightcrawler and Iceman wonder how long it will be before the Church attacks the Xavier Institute. Nightcrawler sees Stacy holding the teleportation net and tells her to put it down. The net suddenly activates and Stacy is whisked away from the Worthington Industries building.
In James Bay, Canada, Wolverine ties his prisoner to a chair and uses scare tactics to get him talking. The priest tells the origin of the Church of Humanity and story of the current Supreme Pontiff :
(Supreme Pontiff’s origin)
Centuries ago, an early American settler, referred to as the “All-Father,” wandered the country and discovered an Indian woman whom he fell in love with. They “joined in a blessed union” and their son was born “under the half-light of a solar eclipse,” making him special. The family lived in blissful harmony with nature until the parents dabbled into the occult and summoned forth a nameless beast from another dimension. The beast was an intelligent, poetry-reciting creature and charmed himself into the family’s good graces and, later, into the mother’s arms. While her son watched in horror, the mother helped the beast kill the “All-Father.” After that moment, the son developed a hatred for everything inhuman. The son studied black magic and killed his mother and the beast, avenging his father’s murder. After that, “he took his first steps toward immortality.” The boy grew into a young man during the Industrial Revolution. After an ominous occurrence, he knew he was destined to become a spiritual leader. Soon after, the future leader met a group of occult scientists. The scientists had built a contraption that allowed the human subconscious to “peer into the mysteries of the universe.” The young man used the scientists’ invention and he was “catapulted across the known planes of cosmic reality.” But the journey was physically taxing and he returned with an injured body. The scientists placed him inside an isolation tank to recuperate. During this time, the young man learned how to control the cosmic energy that merged with his soul, “a force which now powered his humanity.” Once the young man emerged from isolation, the scientists recognized his supremacy and bowed down to him. He became their Supreme Pontiff.
Wolverine finds the story absurd.
Meanwhile, Stacy accidentally teleports into the cathedral of the Church of Humanity and the Church’s followers instantly attack. Stacy fights back, but soon she’s overpowered. Her attackers take her to the confessional.
After hearing the priest’s tale, Wolverine is contacted by Nightcrawler. Nightcrawler tells him that there’s “a situation” and that the X-Men are nearing his position to retrieve him.
While she’s chained upside-down to a wall, Stacy awakens as the Supreme Pontiff speaks to her. The Supreme Pontiff gives another speech on mutant inferiority and he promises Stacy that he’ll have no mercy on her. According to the self-proclaimed holy man, he knows how the universe works, and mutants are unnatural in the cosmic order of things. After Stacy endures some torture, the Supreme Pontiff orders her to tell him about herself and the X-Men. Stacy grants his wish, giving him a story that may be completely fictitious, or a mixture of fiction and truth :
Stacy used to be an ordinary high school girl until her mutant powers kicked in and her skin changed. Subsequently, she became a social outcast and her home life went downhill as well. Her mother’s boyfriend hated Stacy for being a mutant and tried to hurt her. In defense, Stacy’s pheromone abilities kicked in and played with his digestive system. Stacy’s mother was less-than-understanding and kicked her out. Stacy became homeless and found some comfort with other street derelicts. However, when the police tried to break them up for loitering and unlawful assembly, they discovered that Stacy was a mutant. They tried to beat her, but then Professor Xavier arrived and saved the day with his tremendous mental powers. The rest of her story is obviously pure fantasy, as Stacy claims to be one of the original X-Men (instead of Jean Grey), falling in love with Cyclops and fighting with the team for years, before Professor Xavier assigned her undercover work as a madam for the Nevada X-Ranch.
The Supreme Pontiff is not amused by Stacy’s antics and the torturing continues.
Nearby, the rest of the X-Men approach in the Blackbird, homing in on Stacy’s signal. Since the signal is weak, the team fears that Stacy is either nearing death or already there.
From her cell, Stacy tricks one of the Church’s guardsmen into coming close to her. Stacy reaches through the bars and touches him, using her power to chemically render him unconscious.
The X-Men hover over the cathedral and Nightcrawler teleports into the cathedral’s control tower. While the rest of the team lands in the courtyard, engaging an army of the Church of Humanity’s priests, Chamber heads deep inside to save Stacy. Chamber blasts open Stacy’s cell door as his teammates clean house outside.
Meanwhile, Nightcrawler locates the lair of the Supreme Pontiff and the Supreme Pontiff attacks him with an energy blast of unknown power. As Nightcrawler reels on the floor, the Supreme Pontiff sees that Nightcrawler’s a man of the cloth and finds the idea of a mutant priest laughable. The Supreme Pontiff speaks of every creature’s “personal abyss” and decides to violate Nightcrawler’s soul. As Nightcrawler gazes at him in horror, the Supreme Pontiff tells him to surrender what he values most.
Stacy leaves her cell and she and Chamber prepare to leave. Chamber is caught by surprise when he’s attacked by a follower of the Church of Humanity. Nevertheless, Chamber and Stacy manage to subdue the attacker.
Elsewhere in the cathedral, the Supreme Pontiff addresses a legion of his brethren. He speaks of victory and of drawing first blood. Since the cathedral’s soil has been tainted by the presence of mutants, the Supreme Pontiff says that the Church of Humanity must vacate and spread the word elsewhere. Together, the Supreme Pontiff and his followers teleport away.
In an aisle between rows of church pews, Chamber and Stacy meet up with Archangel, Wolverine, and Iceman. With his animal senses, Wolverine detects that the X-Men are alone in the Church. Archangel notices that Nightcrawler’s the only team member missing and wonders where he is. The X-Men find Nightcrawler in the lair of the Supreme Pontiff, unconscious and lying in a fetal position on the floor. Stacy volunteers to help Nightcrawler. Wolverine begrudgingly agrees to let her go to work. Nightcrawler awakens after Stacy uses her power to give him an adrenaline rush. Concerned, the X-Men ask Nightcrawler how he ended up in dire straits, but Nightcrawler remembers nothing of his ordeal with the Supreme Pontiff. The team decides to head home.
Back in the Xavier Institute, the X-Men take a brief respite. Stacy finds a picture of the original five X-Men and makes fun of Iceman’s and Archangel’s old uniforms. Chamber mentions that he hasn’t been in the Xavier Institute for awhile, but Iceman tells him that this team won’t be staying there for long. Stacy heads for the bathroom and Iceman and Archangel take note of her spunk.
Outside, Wolverine speaks with Nightcrawler. Nightcrawler says that, even though his memory fails him, he knows something strange happened to him in the cathedral. He feels that part of his mind has been taken or tampered with. Nightcrawler worries about what he might remember if his memory ever returns.