The presbytery of St. Alipius is a redbrick gothic bungalow built when gold money was still washing through Ballarat. It sits in a Catholic compound of brick and granite schools and convents where the road from Melbourne reaches town. White crosses stand on the gables of the house as if to ward off evil from all points of the compass. The plan, if that was indeed the plan, failed spectacularly.

When young Father George Pell moved his things into the presbytery in 1973, that corner of Ballarat was one of the most dangerous places in Australia for children. Already living in the presbytery was Father Gerald Ridsdale, chaplain at the little primary school standing on the other side of the church. He was raping the children. All four members of the staff, all Christian Brothers, were abusing the children in the school. They would not be exposed for twenty years. George Pell, back from his studies in Rome and Oxford, noticed nothing.

Ballarat was his town. His parents owned the Royal Oak. George Sr. was huge, down-to-earth and Protestant. Lil was fierce, gentle and made all the decisions that mattered in her son's life. She was devoted to the Catholic Church. A portrait of old Daniel Mannix, archbishop of Melbourne since 1917, hung in her kitchen. Her son would one day write: "She was a woman of great strength and faith: a faith I suspect that was very Irish, and probably in particular a faith typical of the west of Ireland in its certainties and in its impatience with theological subtleties." The pub was working-class but not rough. George Sr. ran an SP bookmaking operation out of the front bar and hid the books under his children's beds. He enforced the rules. Children brought up in a pub learn to tolerate all sorts and to value rules. Once they were teenagers, young George and his sister Margaret helped out in the bar in the school holidays but their mother was preparing her children for a life that would take them a long way from the Royal Oak.

Though raised Catholic from birth - tribal Catholic in a town where priests, nuns and brothers ruled the Catholic roost - Lil's big, confident boy had a conversion in adolescence that determined the course of his spiritual life and the trajectory of his career. At the age of fourteen he fell under the spell of B.A. Santamaria:

"As a teenager, probably in 1955, I first heard him talk to a packed cathedral hall in Ballarat on the menace of communism. He set out to identify the mighty forces under the swirl of events. He often appealed to history. We felt we too belonged to the forces of good fighting the new faces of evil, as saints and heroes had done for thousands of years. He placed us in a grand tradition of worthy struggle and combat, where we felt we could do our bit. Some of us never completely lost this conviction."

It was the time of the great Labor Split, the height of the Cold War. Santamaria was at his most mesmerising as he recruited young warriors for the Movement to defend the bulwark of civilisation, the Catholic Church. Communism seemed the enemy when Pell was a boy. Later, when that curse was defeated, it transpired that something just as sinister lay behind its mask: secular liberalism, which had been allowed to take root not only in the world, but in the church. Others might see nothing particularly troubling in the swirl of events, but Santamaria instilled in his followers a habit of discovering everywhere in the world around them a contest between the forces of good and evil.

The boy was "reasonably bright" according to the historian John Molony, who was one of his teachers at St Patrick's, Ballarat. "Unquestionably an unusual human being. Enormously talented in sport. He was a leader, president of every possible organisation in the college." He was big and used his size to get his way. He debated and acted. The grand Pooh-Bah in The Mikado was a role he played more than once in his early years. He ran, rowed and played football with such skill that Richmond offered him a contract in his final year. He signed but had other ideas.

St Patrick's was a great recruiting ground for the priesthood. Pell had shown a religiosity - saying the rosary in the back of the car on the way to football - that was not out of place in the school. Nor was the ambition to have a priest in the family surprising in the pub trade or the Irish tribe from which his mother sprang. Pell says he fought his calling for a long time: "I feared and suspected and eventually became convinced that God wanted me to do his work, and I was never able to successfully escape that conviction." In late 1959 he told his parents he was going to be a priest. His father was hostile. His mother was overjoyed.

So many young men were training for the priesthood that Werribee Park had burst at the seams. These were years of triumphalist high confidence in the mission of the church. Pell found himself among 115 young men living, studying and praying at the direction of the Jesuits in the Italianate pile that housed Corpus Christi College. The place was demanding and inflexible. The saying at Werribee was: "You keep the rules and the rules will keep you."

Pell thrived. He liked this life and Werribee has remained, ever since, his model for the proper training of young men for the priesthood. Roughhouse antics were not unknown. Sport and amateur theatricals were part of the program. But Werribee demanded prayer, lots of prayer. Pell's superiors admired the young man's forthright ways and eagerness for responsibility. In his third year he was put in charge of the discipline of new arrivals. There were those among the underlings who found him harsh, formal and unforgiving. Pell's reputation as a bully dates back to Werribee. But those closer to him remember more vividly how certain he was of his faith. He never criticised. He never doubted. "He is a guy for whom it has always been very clear," recalled Brian Scarlett some forty years after their time together in the seminary. "He was exactly the same as he is now."

Sir James O'Collins, the bishop of Ballarat, had his eye on young Pell. O'Collins had been bishop since World War II, was a close friend of Santamaria's and had been a leader of the Movement from its early days. Santamaria valued the bishop not least because he had once been an active member of the Plumbers Union. O'Collins was a straightforward man who loved the life of bishop. Seeing in Pell the makings of a champion, he was the young man's first patron. Pell called him: "father and friend to me, [he] sponsored my progress and offered me marvellous educational opportunities." In 1963 he plucked Pell out of Werribee and sent him to study at Propaganda Fide in Rome.

Vatican II was underway. Pell, swept up in the hopes and drama of the Council, counted himself in those days as "deeply committed to its liberal reforms." His Italian was soon serviceable. He loved the city; its pomp and its history. From this point, Rome would be his other country. He would always have a life there. In December 1966 he was ordained at St Peter's - his father stayed home to look after the pub - and the following year he presented a rather edgy dissertation defending the theology of Teilhard de Chardin for which he was granted high honours. After a summer working in a wealthy Baltimore parish, he arrived at Oxford. This was all part of O'Collins' plan: he wanted a formidable intellectual who could come home and take on the Catholic academics who continued to oppose the Movement.

Oxford changed Pell. It's an old story: he was seduced by English ways and English high culture. Oxford buffed and polished the boy from Ballarat. He came to see his years in the university town as at least as formative as his time in Rome. For the only time in his life he wondered if there was a God. "I came to understand the intellectual force of alternative views, of agnosticism," he told Luke Slattery of the Australian. Pell was not living in secular Oxford but at the Jesuits' Campion Hall, where he spent four years writing a thesis on the struggles of the primitive church against heresy. The Exercise of Authority in Early Christianity from about 170 to about 270 earned Pell a doctorate and marked him for life not as a theologian, but a historian of the church. He knows theology, of course, but he brought to the controversies of his career the conviction that the beliefs and practices of the church were right because they were old. He was derided by his critics for this, but he came to see the church as essentially untouched by time.

No one could know this then, but the decade Pell spent in Werribee, Rome and Oxford marked a high tide for Catholicism in the modern West. At the age of thirty, with remarkable qualifications and great things expected of him, Pell was returning to Australia to work as a priest just as Catholics began to desert their church. He was a kid seminarian when the Pill hit the market. He had his head in the turmoil of the third-century church when Paul VI reaffirmed Rome's absolute opposition to contraception. Humanae Vitae brought rebellion to the pews. Attendance at mass began to fall away. Those who stayed did what Vatican II had said they could: decide the matter according to their own consciences. In the struggle with pleasure inside the Catholic Church that began with Paul's encyclical in 1968, dogma lost.

Pell's liberal spring was soon over. He joined the pessimists like Santamaria who feared for the church if "the principle of the moral autonomy of the individual" was allowed to override the authority of the pope. "Within fifteen years," wrote Santamaria, "the forces unleashed by that principle had eroded the foundations of Catholicism throughout the Western world."

Pell set himself against conscience and for authority. Rarely from this time would he preach or write without taking a swipe at conscience and reminding Catholics of their obligations of obedience. It would win him few friends, many enemies and high office.

This is an edited extract from Quarterly Essay 51, The Prince: Faith, Abuse and George Pell by David Marr, out today.

David Marr is a multi-award-winning author and journalist. He has written two previous bestselling biographical Quarterly Essays, Power Trip: The Political Journey of Kevin Rudd and Political Animal: The Making of Tony Abbott.