The papal plane is heading for Mexico and John Paul II is busy preparing for the first of his many overseas trips. It is January 1979. At his right hand, briefing him, is the Mexican-born Father Marcial Maciel Degollado, founder of the ultraconservative Legion of Christ, one of the youngest but fastest-growing religious orders in the Catholic Church. This dapper, well-connected priest, worshipped by his adoring followers as "Nuestro Padre" ("Our Father") shares with the Polish pontiff a conviction that the liberal reform of Catholicism in the 1960s needs to be halted, especially in Latin America.

That trip was the first public sign of the extraordinary bond between Maciel and the man in charge of a church of 1.2 billion souls. In the subsequent 26 years of John Paul's reign, the Legion was regularly lauded by him for its unwavering fidelity to church teaching, its intolerance of dissent, and its conviction that only Catholicism could save the world. Maciel was a prince of the Church, in the papal inner circle, sitting on the most important Vatican committees and running his own congregation of 800 priests and 2,500 seminarians, plus the 70,000 lay members of the associated Regnum Christi movement, as it spread around the globe, including a base in London.

Much has been made of the power wielded by the secretive Opus Dei under John Paul II, not least by Dan Brown in The Da Vinci Code, but many Vatican-watchers believe that the Legion of Christ was bigger, richer (annual budget £435m), more influential, and even more sinister.

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Parents of youngsters recruited as Legionaries described it as a cult that targeted the young and naive in particular, some of them just 13, and then "brainwashed" them. But it is Maciel himself who has proved most controversial. Nuestro Padre was, according to one biographer, "a narcissistic sociopath" with a taste for flights on Concorde and five-star hotels. He is acknowledged by the Legion to have fathered at least one child – a 23-year-old daughter said to be called Norma Hilda and now living in Madrid.

It has also been alleged that he was a paedophile. The first accusation came in 1976 from the former head of the Legion in the US. By 1998, the Vatican had received sworn statements from eight men, all detailing how Maciel had abused them when they were young recruits.

Throughout the 1990s, a series of allegations of sexual abuse of minors by priests that had been covered up by the church authorities shook Catholicism in America, Canada, Australia, Ireland, the UK and other countries. At least two cardinals were forced to retire, dozens of paedophile priests were jailed for their crimes, and the Church paid out millions of pounds in compensation to victims. The damage to its reputation in the eyes of its own congregations has been huge, and bishops have struggled to convince sceptics that they have put into place procedures rigorous enough to ensure that such a betrayal never happens again.

Yet in Maciel's case, it took 30 years – until 2006, after John Paul's death – for the new pope, Benedict XVI, finally to issue a public rebuke, and then it was simply an order that he should see out his days in private prayer rather than face a court. The long delay is evidence, some have suggested, that the Vatican still does not take the issue of paedophile priests sufficiently seriously.

A year after Nuestro Padre's death in 2008, the Vatican announced an investigation into the Legion. An unnamed official told America's National Catholic Reporter newspaper that the total number of Maciel's abuse victims was "more than 20 and less than 100". As a team of cardinals opens the locked cupboards of an organisation that prided itself on secrecy – all new recruits had to take a unique private vow (abolished by Benedict in 2007) never to speak ill of the founder and to report to superiors anyone who did – the Catholic Church is once more mired in a scandal about the sexual abuse of minors, and the abuse of power.

Ex-priests and nuns are often easy to spot. It is something to do with how uneasy they look in civvies, and their reluctance, learnt in the seminary and the convent, to look anyone in the eye. But Todd Carpunky, a corporate lawyer in the City of London, gives few outward clues of his past as a Legionary of Christ when we meet in a bar near Liverpool Street station. Tall, blond and open-faced in his well-cut suit, this Illinois-born 34-year-old has an easy sense of humour, both about the world around him, and his six years in the Legion. "My grandmother raised me," he explains. "She was great, but so Catholic she makes the Pope look like the anti-Christ. The rest of my family was just nuts. I wanted to get away from them, and the Legion knew that."

Founded by the then 21-year-old Maciel in Mexico in 1941, almost four years before he was even ordained as a priest (he had been asked to leave more than one seminary), the Legion of Christ spread rapidly, supported by bishops who felt embattled by government anti-clericalism in Mexico, the result of a church-state spilt in 1917. Soon it was running schools and universities. Its militant, old-style Catholic spirituality was directed mainly at the wealthy with the result that it members were known as "the Millionaries of Christ".

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By the 1950s, it had gone international with branches in Spain, Chile, Italy, Ireland and the United States. Carpunky came across one of its recruitment drives in the early 1990s via his grandmother. "They began visiting me at home and invited me on a summer programme. It was fun and my grandmother was delighted. She's still upset I'm a lawyer." He went to one of the Legion's boarding schools in Connecticut at the age of 16, seeing it as a means of escape from an unhappy home life. "Our contact with home was strictly limited, but that suited me. All our mail was reviewed. Even the Catholic newspapers were censored. They would have great holes in them where articles had been cut out. It was to protect our vocation, we were told."

Life at the school followed a strict schedule. "We'd get up early in the morning, shower with our bathing suits on, even though there were curtains, because apparently it was faster and more chaste. We slept in our swimming trunks under our pyjamas. There was meditation – usually on the writings of Nuestro Padre. It was all very regimented. We were not allowed free time. It was cult-like. Maciel played mind games."

All of this, Carpunky acknowledges, is said with the benefit of hindsight. At the time, he quickly moved into the noviciate and was sent to Spain to train as a priest. "I felt part of something. I was happy. I didn't rationalise."

What was Maciel like? "He had charisma. He told great stories. He was the great conspiracy theorist. According to him, he had left the seminaries in Mexico because he was misunderstood and was trying to save the Church. The Jesuits, he said, were very jealous of him. He used conspiracy theories to explain away all of these things. He had been persecuted because he was just too holy, too clever, too Catholic. He actually claimed never to have said no to God – which implies he never sinned."

Maciel was also, Carpunky claims, intent on controlling every aspect of the life of every Legionary. "We had a green book of rules of etiquette and social norms," he recalls. "We'd have classes about not piercing a vegetable with a fork when we were eating, or how to eat a banana with a knife and fork."

Carpunky was singled out for attention by Maciel. "When he came to Madrid, I was asked to serve his meal. I took it as a great honour. I thought he was a living saint. So when he would follow me with his eyes, I thought he was looking into my soul. Now I think he was checking me out because apparently he liked blonds."

The first major question mark was raised over Maciel's personal conduct as early as 1956, when he was suspended by the Vatican while charges that he was addicted to pain-killing drugs were investigated. Two years later, the inquiry was dropped and he was reinstated. Then, in 1976, Father Juan Vaca, who had joined the Legion as a 10-year-old in Mexico and risen to be its US director, but subsequently left to work as a priest in a Catholic diocese on Long Island in the States, formally reported Maciel to his bishop for sexually abusing him from the age of 12. This was a time before the sexual abuse of minors by priests had been exposed. In 1978, fearing that his accusations had been swept under the carpet, Vaca sent a long statement about what had happened to him direct to the Vatican, and even received an acknowledgement. And then, nothing.

In 1998, eight other former members of the Legion (one now dead) filed sexual-abuse charges against Maciel in the Vatican's Court of Canon Law, but Rome seemed to delay. It was only in 2004 that an official investigation, headed by canon lawyer Monseigneur Charles Scicluna, was set up. That led, in 2006, to the decision to discipline Maciel.

Was Carpunky sexually abused? "I am one of the few people who has been in Maciel's bedroom without... you know... because he has a bedroom in each of the Legion's houses, reserved for him. In the American house at Cheshire in Connecticut, he even had his own Mercedes reserved for him 'because of his back problems'. He always had these weird things. He could only drink Evian water. For medical reasons, he'd eat only steak or a specific type of chicken that had to be obtained from Spain. I wasn't sexually abused, though a friend of mine in seminary had been molested by a Brother in the Legion in his early teens. When the rector found out, he told Maciel, and within 24 hours that Brother was sent to Rome, where he was later ordained as a priest."

It raises the suggestion of a culture of sexual abuse inside the Legion, taking its lead from the founder and covered up by the "private vow". Carpunky is not convinced. "Maciel was a monster and others were abused, but they were more the exceptions than the rule."

Consider, though, the experience of Stephen Dougan – not his real name – from Belfast. Now a university student, he was wooed by the Legion as a 14-year-old. "It was hard not to be enthused by what you were shown," he recalls. "As their guest, I enjoyed good food, went on hikes, played table tennis, watched movies and did sport with happy seminarians. When I actually joined [in the early 1990s at the Legion's Dublin seminary], I did not have even a vague idea of the Legion's spirituality or its rules, only that, as I was being told, I had been called as part of God's plan."

Around the time of his 18th birthday, Dougan was summoned one night to the bedroom of his novice master. "He said he had severe cramps in his stomach. He unbuttoned his pyjama top, poured oil on his stomach and asked me to massage him. I did. Very soon he unbuttoned his pyjama bottoms and poured on more oil. He asked me to 'do it deeper'. He meant lower down. His penis was erect. I was shocked and confused. I can remember my hands in his pubic hair. I closed my eyes and prayed."

Dougan's abuse by the Father almost exactly mirrors allegations against Maciel, made by Fernando Perez, one of the eight to file charges, about what happened to him at 14. Maciel even told his victims, one reported, that he had a special dispensation from the Pope to allow him to be masturbated because of the pains he suffered as a result of his "delicate" health.

Dougan never spoke while in the Legion about what had happened, though he has subsequently reported it to the police. "The vow I had taken meant that no Legionary could in any way criticise the defects or mistakes of any superior. This included internal – in your mind – criticism." Eighteen months after the incident, he was told that he didn't have a vocation and asked to leave. "It was hard for me to adjust to normal life," he admits. "I am still battling with the belief that God has spat me out of his mouth because I left. I have been in counselling on and off ever since."

Not all ex-members – some of whom belong to the support group, ReGain – have unhappy memories. Adam Dunbar – he is not willing to use his real name because he is still in touch with former colleagues from in the Legion – is a 62-year-old bookkeeper and grandfather from Dublin. He was among the first recruits to the Legion's Irish mission which started in 1960. "What attracted me as a youngster was the energy of it, the ability to inspire, and the fact that they used young men to recruit young men and filled us full of idealism." Maciel, he reports, was "gentle, considerate, patient. My memories of him are sweet. I never had any experience of anything irregular nor did I see anything that in retrospect might be judged as misbehaviour."

Matthew Muggeridge, the 39-year-old grandson of the celebrated writer and broadcaster Malcolm, is currently working as a lawyer in the US. He joined the Legion in 1990 because he saw it as "dynamic, challenging and growing. It enthused me about my faith – and you don't get that with ordinary diocesan seminaries." Though he left six years later, he did so, he says, with no regrets and remains a supporter of the order and its defence of traditional Catholic values.

He was part of Legion plans to establish a base in London. Still a seminarian, he was sent to the affluent parish of St James, Spanish Place, in Marylebone, central London, along with an Irish Legionary priest. However, Cardinal Basil Hume, head of the local Westminster archdiocese, was not keen on their presence, Muggeridge recalls. "He tended to equate the Legion with Opus Dei, about which he also had well-recorded concerns, but we were not the same. We were so visible, whereas Opus Dei tends to act behind the scenes." The Legion is still thought to have ambitions on London. In the past year, one of its priests has been calling on parishes in wealthy areas of the capital.

Maciel had prepared himself a tomb in Our Lady of Guadalupe, the church he built in Rome in the 1950s. In the event, he was laid to rest in January 2008 in his family's modest crypt in his hometown in Mexico. The past 18 months have been a traumatic time for Legionaries. The secrecy rules meant they knew nothing of the charges against Nuestro Padre. The first they heard was when, a year after Maciel's death, Father Alvaro Corcuera, his hand-picked successor, confirmed the existence of Norma Hilda.

The Legion is tight-lipped about its current predicament. Jim Fair, its communications director, declined even to discuss the issues raised by the former Legionaries in this article. In brief written answers to questions I submitted, he said that the Legion was "grateful" for the present Vatican investigation and "sad" about the "aspects of our founder's life of which we were not aware". On the charge that the order has a cult-like approach, Fair wrote: "We listen carefully to what former members have to say. At the same time we listen to the voice of the Church and to the principles of religious life throughout the centuries as a guideline."

Adam Dunbar feels the revelations will have had a profound effect on his friends still in the Legion. "Imagine, after half a century of being told that Maciel was a living saint, you discover that this is a hall of smoke and mirrors. Who is the victim then? Apart from the sexual abuse, if it existed, what about this abuse of lives?"

Back in the City of London, Todd Carpunky has, he says, put the Legion (and his Catholicism) behind him. His doubts began when he contracted a liver infection because painful gallstones had gone untreated. His superiors advised him instead to swim and pray to Mary. Later, he was made to wait several months for an operation on a disc problem in his back that had left him disabled, because Nuestro Padre couldn't decide what to do with him. "The final straw came when I was sitting in a doctor's office and the Legionary with me admitted they had been lying about not being able to find a surgeon to see me. I was told, 'Just obey.' That's when I snapped and realised they were crazy. I checked my brain back in and left."

For him, the story of the Legion is not just another aspect of clerical sex abuse. "It really comes down to the fact that they cared more about building the Kingdom of Maciel than the Kingdom of God. The Legion calls itself Catholic but it is inhumane and really damages people. That is what distinguishes it from other religious orders." n

A catalogue of abuse

Britain Father Michael Hill (pictured) was convicted in 1997 of sexual abuse of nine children. It emerged that his local bishop, the future Cardinal Cormac Murphy-O'Connor, had been aware that concerns had been raised about Hill's behaviour, but had moved him to another parish.

US Allegations of sexual abuse of minors by Catholic priests were first made public in 1984. In September 2003, the archdiocese of Boston paid $85m in compensation to 552 victims. Many other dioceses have made similar payments – to an estimated total of $1bn. In 2004 the archdiocese of Portland declared itself bankrupt as a result.

Austria Cardinal Hans Hermann Groër was dismissed as Archbishop of Vienna by Pope John Paul II in 1995 after it emerged that he had abused young boys at Catholic schools over a 40-year period. One expert suggested he may have had 2,000 victims.

Ireland In May 2009, High Court judge Sean Ryan published a report of his nine-year investigation detailing the beating, rape and humiliation of thousands of children by priests and nuns in the schools they ran.

Australia In July 2008 in St Mary's Cathedral in Sydney, Pope Benedict XVI made an unprecedented apology for the crimes of priests against minors. "I am deeply sorry for the pain and suffering the victims have endured and I assure them that, as their pastor, I too share in their suffering." PS

The papal plane is heading for Mexico and John Paul II is busy preparing for the first of his many overseas trips. It is January 1979. At his right hand, briefing him, is Mexican-born Father Marcial Maciel Degollado, founder of the ultraconservative Legion of Christ, one of the youngest but fastest growing religious orders in the Catholic Church. This dapper, well-connected priest, worshipped by his adoring followers as 'Nuestro Padre' ("Our Father') shares with the Polish pontiff a conviction that the liberal reform of Catholicism in the 1960s needs to be halted, especially in Latin America.

That trip was the first public sign of the extraordinary bond between Maciel and the man in charge of a church of 1.2 billion souls. In the subsequent 26 years of John Paul's reign, the Legion was regularly lauded by him on account of it unwavering fidelity to church teaching, its intolerance of dissent, and its conviction that only Catholicism could save the world from ruin. Maciel was truly a prince of the Church, in the papal inner circle, sitting on the most important Vatican committees and running his own congregation of 800 priests and 2,500 seminarians, plus the 70,000 lay members of the associated Regnum Christi movement, as it spread round the globe, including setting up a base in London.

Much has been made of the power wielded by the secretive Opus Dei under John Paul II, not least by Dan Brown in The Da Vinci Code, but many Vatican-watchers believe that the Legion of Christ was bigger, richer (annual budget £435 million), more influential, and even more sinister.

Parents of youngsters recruited as Legionaries described it as a cult that targeted the young and naive in particular, some of them just 13, and then 'brainwashed' them. But it is Maciel himself who has proved most controversial. Nuestro Padre was, according to one biographer, 'a narcissistic sociopath' with a taste for flights on Concorde and five star hotels. He is acknowledged by the Legion to have fathered at least one child – a 23-year-old daughter said to be called Norma Hilda and now living in Madrid.

It has also been alleged that he was a paedophile. The first accusation came in 1976 from the former head of the Legion in the US. By 1998, the Vatican had received sworn statements from eight men, all detailing how Maciel had abused