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The Supreme Pontiff is a hard character to summarize. He/she was used by only two writers ( Joe Casey and Chuck Austen) who gave very different depictions of the character. Concerning its sexual identity, background, ideology and status as a superhuman. Below are brief summaries of the two accounts. 

Foreshadowing

 
 In "Uncanny X-Men" #395 - 398 ( August - November,  2001), a group of X-Men ( Archangel, Chamber, Iceman, Nightcrawler, Wolverine) faced a new foe in the sewers of London. Calling himself Mr. Clean, the man set mutants on fire with a flamethrower to exact his own style of "genetic cleansing" or "purification" of them. While the man was eventually killed by Wolverine (set on fire), Clean was revealed as a single agent of a much larger organization. Calling themselves "Church of Humanity" and headed by a Supreme Pontiff.
 
In #399 (December, 2001), the main operatives of the Church of Humanity were seen for the first time. They were dressed in identical uniforms, concealing their identities. They operated as a small army equipped with teleportation devices, laser guns and bombs. They targeted the X-Ranch of Nevada, a brothel run and staffed by mutants. They managed to slay most of the staff and human clients inside despite stiff opposition by two X-Men present (Archangel and Iceman) and one of the prostitutes ( Stacy X). The latter trio were the only survivors of the operation.

Origin 1

 In #400 (January, 2002), This group of X-Men (Archangel, Chamber, Iceman, Nightcrawler, Stacy X and Wolverine) decided to be proactive and track down the leadership of the Church. The next attack by Church operatives took place in Atlanta, Georgia, targeting the researchers of a gene laboratory considered too friendly to mutants. This time the X-Men reacted in time, forcing the fanatics to retreat. But Iceman managed to capture one alive. 
 
Following an interrogation by Wolvie, the prisoner narrated the Supreme Pontiff's origins. (Told in an extensive flashback sequence). He had been born centuries ago, the son of a mixed marriage. His father was an early American settler, seeking his fate in the wilderness of North America. His mother was a Native American of unspecified tribe. The boy was born under the half-light of a solar eclipse, somehow making him "special".
 
The little family lived in isolation but "at harmony with nature". Until the parents turned to occultism. Managing to summon forth a nameless other dimensional "beast".  It did not seem threatening. It was intelligent, eloquent and even poetic. It charmed them. Right before seducing the mother of the family. The two lovers eventually murdered her husband. Horrifying the young boy. He started hating the beast, a hatred which later grew to include everything "inhuman". (Mutants included).
 
The boy started studying black magick. Advancing enough to kill his own mother and her beast. His first step towards immortality. The boy grew into a young man during the Industrial Revolution (1760s - 1890s by most estimations). He understood his role to become a spiritual leader. He joined a group combining science with the occult arts. He was the test subject in an experiment which would allow the human subconscious to "peer into the mysteries of the universe".
 
The experiment left him with an injured body but bathed his soul in "cosmic energy". An energy he learned to use. Once his body recuperated enough, his former colleagues realized his supremacy. Bowing before him as mere servants. He became the Supreme Pontiff of their group. 

Meeting the X-Men

 
The same issue introduced the modern version of the Pontiff. Ruling his organization from his Montana headquarters. Preaching to followers offering their lives and souls to him in exchange for "ultimate salvation". Declaring the ultimate cause of their organization to be the complete eradication of mutants, maintaining the supremacy of the humans (homo sapiens).
 
The X-Men were trying to understand how the teleportation device they had confiscated from the prisoner worked. Stacy X accidentally turned it on, teleporting to its last programmed destination. The Church of humanity headquarters in Montana. The Pontiff wasted little time in capturing her, torturing her and interrogating her. He wished to learn more of her and her allies. She offered him an account which mixed her own life-story with that of Jean Grey
 
While the Pontiff wasted time listening to her, the rest of the X-Men were tracking down Stacy's mutant signature. They were soon able to invade the headquarters and found the unprepared and under-equipped "priests" to be much easier opponents. 
 
Nightcrawler was the one to track down the Pontiff. The Pontiff attacked him with an energy blast which left Kurt reeling on the floor. Instead of finishing his opponent off, the Pontiff started playing mind games. He ridiculed Kurt's aspirations as a man of the cloth. He then spoke of the personal abyss within every creature, housing their fears and their answers. (Their belief system?) He somehow looked within the horrified Kurt, searching for what the mutant valued most.
 
Nightcrawler was next found alone in a fetal position. He had no real memory of his encounter with the pontiff. But felt that something had been taken from his mind. Fearing to ever realize what it was.

Lasting Effects

 
The Pontiff subplot was followed in #407 (August, 2002). Nightcrawler suffering of nightmares involving his own crucifixion by the Church of Humanity and the Pontiff repeating the same enigmatic phrase "taking away what means most to you".
 
Recuperating at the time with an old circus friend in the Bavarian Alps, Kurt exhibited doubts concerning his role in the X-Men. Commenting on isolation with no friends or enemies as a way to achieve peace of mind. Bitter that Professor X only uses him as a field operative, never a teacher. He admitted having doubts of Xavier's Dream. He was no longer at peace with his choices in life.
 
In #409 (September, 2002), while investigating the Vanisher's drug cartel, Nightcrawler was horrified to find the basement of St. Paul's church filled with corpses, the remains of junkies. He confronted the resident Cardinal. Finding out the high-ranking priest was also a junkie. The Cardinal demonstrated a mutation turning him to bestial form. Nighcrawler was almost killed in combat by the creature. Saved at the last moment by agents of the Pontiff. They were sent to execute the Cardinal. They did not dare touch Kurt as the Pontiff had "plans" for him

Reintroduction

 The Church was reintroduced in  #422 (June, 2003), An archaeological expedition including Havok, Nightcrawler and Polaris had managed to locate evidence of an ancient mutant civilization within the Bermuda Triangle. Operatives of the Church attacked in order to destroy said evidence. Their equipment exploded, killing them. Leaving vague if it was suicide or Lorna decided to kill them. (Both ideas introduced in the same page).
 
#423 (July, 2003). Church operatives had somehow managed to crucify six mutants, right on the front lawn of the Xavier Mansion. Recognizable among them were Jesse Aaronson, Jubilee, Magma and Skin. The two ladies survived, the men were not so lucky.
 
Cyclops soon called a meeting of all X-Men present to discuss any hints as to the identity of their opponents. Havok identified them as "the idiots in the priest costumes". Nightcrawler clarified that the name was "Church of Humanity" and his squad was quite familiar with them. Enraging Scott since nobody had bothered to bring them to his attention, nor to that of anyone outside Kurt's group. 
 
The conversation turned to Nightcrawler's recent activities. He mentioned renouncing his priesthood. Getting bewildered stares from all X-Men present in the room. Nobody was aware of Kurt ever being a priest. (Nightcrawler's priesthood had been introduced as a plot point in "X-Men" vol. 2 #100 - May, 2000). Soon it was established that memories of his ordination were simply memory implants. 
 
Soon a group of X-Men  ( Cyclops, Havok, Iceman, Nightcrawler, Phoenix, Polaris and Wolverine) headed for the place of his "ordination", St. Michael's Church in Brooklyn, New York. (Also introduced  in "X-Men" vol. 2 #100). The building seemed abandoned for quite a while. 
 
A quick investigation by Jean revealed that appearances were deceiving, the basement contained a secret laboratory full with the bodies of mutants. Some were dead, others were dying, a few alive but in pain.

Finale

 
In #424 (July, 2003), the X-Men had their final confrontation with the Church and its Pontiff. Revealing his/her plans for Kurt and a different background story. 
 
The Pontiff was revealed to have used an illusion-casting mutant, "Mutant 143", to tamper with the mind of Kurt. She had been impressed with Kurt's love of God and his ability to hide his Satanic appearance through use of an image inducer. She was grooming him to become the next Pope of the Roman Catholic Church. In time, an arranged failure of the inducer would reveal to Christians that their beloved Pope was Satan himself.  
 
Killing two birds with one stone. The Catholic Church would collapse and mutants would be firmly identified as agents of the Antichrist. Forever hunted down. Without spiritual leadership, the Western world would search for solace elsewhere. Right in the hands of the Pontiff. A complex plan ruined because Kurt could not control his sexual urges enough to play priest.
 
A bit later the next step to that complex plan was revealed. They would set up a  false Rapture. Defined here as "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." While the issue identifies this as part of the Catholic belief syste, it clearly isn't. It is a 19th-century, Protestant religious idea, mostly originating in the writings of John Nelson Darby (1800 - 1882).
 
The Church of Humanity would orchestrate events to make it appear the time of the Antichrist has come.  Pious Catholics around the world would vanish in the blink of an eye. Because the Church had tampered with their Holy Communion. They would consume a substance guaranteeing their "disappearance". Actually disintegration. For those left behind, a Savior (Messiah) would be needed. The Pontiff would gladly offer her services to the horrified crowds.

Origin 2

 Nightcrawler and the Supreme Pontiff enganged each other while exchanging Biblical phrases and condemning each other's self-righteousness. Removing the Pontiff's hood, she was revealed as a woman. Shocking Kurt but having Iceman commenting on her cute appearance. She was killed in an explosion shortly afterwards, refusing to take Kurt's hand to escape.
 
The X-Men later investigated her background. She was once a Roman Catholic nun. Raped by a lustful priest, she was punished instead of him. He accused her of breaking her vows and had her thrown out of monastic life. She loved religious service and had actually never wanted to leave. All her plans were in effort to take revenge against the church officials who wronged her. 

Conclusion

 
The two different depictions of the Pontiff are hard to reconcile. A centuries-old immortal man and a young woman, a supernatural creature and a common human with access to advanced technology, a subtle manipulator and a vengeful maniac. One wonders if there are two Pontiffs.

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