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The German town of Freising is overlooked by a hill called the Domberg. It is dominated by a twin-towered Romanesque Cathedral. Just off to one side is a museum to Pope Benedict.

It is little more than a corridor with a few photos. One stands out. It is of a young man in uniform. He looks past the camera. The stare is empty, expressionless, at a time when safety lay in a vacant look that could not be read. Joseph Ratzinger is 16, an assistant in an anti-aircraft unit in the Wehrmacht. Hitler's Imperium is drawing to a close.

A short while later the young man is in a seminary. His face is lively, absorbed, immersed in books. He is the stand-out scholar of his generation and his peers know he is destined for Rome.

The gallery of pictures is thin. Joseph Ratzinger left few visual traces as he rose from Bavarian priest to become the leader of the Roman Catholic Church. He was and remains, at heart, an academic. Recently he told Professor Wolfgang Beinert, his former assistant, that his times teaching had been his "most important days". "I was at my prime," he said. Beinert's view is that the Pope remains "a professor down to his boot straps".

When he was elected Pope in 2005 the crowd began shouting "Benedictus! Benedictus!" He recoiled from the adulation. "I am not the main event," he said. He was a reluctant pope who, before he was chosen, had confided to friends that he longed to retire to Bavaria and to walk the hills.

But this elderly academic, who one ambassador likened to a "grandpa", presides over a Church buffeted by scandal. On an almost daily basis there are revelations of priests abusing children. Last Friday a dossier was released in Belgium cataloguing the grim details of abuse of children as young as two. In Belgium they say this is the Church's "Dutroux", referring to a paedophile found guilty of six rapes and four murders.

And from the sidelines, and makes the charge that perhaps 100,000 children have been abused.

In a square near the Pantheon in Rome I meet a priest. He is an older man, familiar with the ways of the Vatican. He has no doubt in his judgement. "I think," he says, "it is the most serious crisis since the Reformation". In 1517, when Martin Luther nailed his theses to the church door in Wittenberg, it shook the Church to its core and ushered in the Protestant Reformation.

Time and again in Rome and elsewhere I found people asking the same question: "Is the Pope up to the challenge?"

Pope Benedict is not reclusive, but he has lived simply. He plays the piano, especially Mozart. The British Ambassador to the Vatican, Francis Campbell, says: "He lived outside the Vatican walls... in an apartment with a cat, a piano and his books. In the months after he became Pope, one of his neighbours says she saw him return to his flat to see the cat and play the piano."

Ambassador Campbell says: "He is one of the greatest intellectual minds to have inhabited the papacy for two to three hundred years. He is a member of the French Academy."

Joseph Ratzinger is conservative by instinct. "My heart beats Bavarian," he once said. During the 1960s he favoured reform, finding the Church too bound by rules, but the student riots of 1968 changed him. According to Beinert, his assistant, Joseph Ratzinger saw in the protests "an atheistic world, which lacked any form of godliness or spirituality". "I stared into the ugly face of atheism," Ratzinger said later. Beinert says "he switched back to the more traditional values of the Church and fighting secularism became his mission".

Later he became the prefect in charge of one of the most important bodies within the Church, . It is the successor to the Inquisition. Ratzinger was the enforcer, uncompromising, cracking down on dissidents within the Church. It earned him the name God's Rottweiler.

As Pope he has taken a strong line against women priests, contraception and homosexuality. He has had his controversies, like when he quoted a Byzantine Emperor who characterised some of the teachings of the Prophet Muhammad as "evil and inhuman". He later claimed that his use of the quotation had been misunderstood.

But the sex abuse scandal is eating away at the Church's moral authority. In parts of the world the revelations have driven away congregations. In Ireland, where almost a third of the population once greeted Pope John Paul II, they are struggling to sell tickets to see Pope Benedict in London.

While a cardinal, he took steps that were intended to signal zero tolerance of sexual abuse. "He was the first to see the seriousness of the issue," said Ambassador Campbell. But Cardinal Ratzinger wanted investigations to be handled internally and for priests to face canon law, rather than criminal prosecution. He remains very protective of the Church's power.

knows the Pope. He says of the abuse: "These were criminal acts, covered up by many, not just by individual bishops. The Pope himself wrote a letter ordering the matter to be dealt with internally by the Church.

"The Pope should apologise. He should say 'mea culpa'. The whole thing reveals a wrong attitude towards sexuality. But also the wrong attitude towards authority. The Church needs to be more transparent, open and democratic. We need a more open Church - not just a Roman system of imperial power."

I meet Monsignor Mark Langham at . He is unusually candid. "As a priest, I have had my confidence shaken," he tells me. "It is difficult for the Church to get hold of this issue." But, he adds, the Holy Father "has made it very clear that we can't accept this sort of behaviour".

The Pope has apologised and has met victims of clerical abuse. Earlier this year in Malta he was said to be close to tears.

Hans Kung insists the Pope has the means to radically reform the Church. "The Pope is more powerful in his Church than the president of the United States is in his country," he says. "The Pope could change overnight the rule of celibacy and it would be changed. But if he does not want to change? Then nothing happens."

Monsignor Langham disagrees. "People misunderstand what the Pope can do," he says. "He can't change the whole agenda. The Church has a much deeper, and a very proud, history of faithfulness that makes it very hard to change. This Pope and any future Pope are very unlikely to bring about change. Their area of movement is very limited. It is not that he can say something and it is done. The tradition of the Church does not allow him to do that."

And personally the Pope is wary of reactive change. He does not want a Church that trims its message to suit the times. His time-frame is the span of centuries. Francis Campbell notes that the Catholic Church is "the world's oldest organisation". "Perhaps the Pope's attitude to change is that we have got something right ... if we are still here today?" he asks. The Pope's preoccupation is with the future of the West and how secularism is undermining its values.

In Rome I stand on a rooftop with an Opus Dei priest. There are magnificent views of the Eternal City. He points out some of the 400 churches and seminaries. He takes comfort from the fact that most of the abuse cases go back more than 20 years but that does not answer the questions "why?" and "why so many?".

Back in Bavaria I sit down with one of the Pope's former students. They are friends and still meet. He gives me a signed picture from the Pope. Within 10 or 20 years celibacy will be dropped, he tells me. It does not exist within the Eastern Catholic Church. I express surprise. It is inevitable, says the priest, with the wave of a hand. I wonder aloud whether the Pope might contemplate such a change. "With this Pope, it's impossible," he tells me swiftly.

Beneath the surface, there is a clamour for change. Robert Mickens from says that increasingly parishes are going their own way. Unofficially there are women priests in the US. He raises the possibility that the Church may even split.

I drive along the Appian Way to the Albana hills and Castel Gandolfo, the Pope's summer residence. The Pope is holding his Wednesday audience in the town square. There are people from all over the world. Some are dressed in traditional costume. Some have lugged statues of Mary from their local churches so that they can be blessed. There are brides in extravagant wedding dresses who hope that merely being in the presence of the Pope will bless their marriage.

As the audience begins, messages are read out in different languages indicating some of the groups who are in the square. When their names get mentioned they let out a cheer and the Pope waves to them. Afterwards several people said they liked his smile, his humility.

In the early autumn sunshine it is tempting to believe that the Church - with its long view of history - could emerge from this scandal unchanged. But then I recalled the Pope's Bavarian friend who said to me: "We can't find the priests. There are dioceses here that have no new candidates for priesthood. The churches are empty."

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