How do you atone for something terrible, like the Inquisition? Joseph Ratzinger attempted to do just that for the Roman Catholic Church during a grandiose display of Vatican penance – the Day of Pardon on March 12, 2000, a ritual presided over by Pope John Paul II and meant to purify two millenniums of church history. In the presence of a wooden crucifix that had survived every siege of Rome since the 15th century, high-ranking Cardinals and bishops stood up to confess to sins against indigenous peoples, women, Jews, cultural minorities and other Christians and religions. Ratzinger was the appropriate choice to represent the fearsome Holy Office of the Inquisition: the German Cardinal was, at the time, head of its historical successor, the Congregation for the Doctrine of the Faith. When his turn came, Ratzinger, the church’s premier theologian, intoned a short prayer that said “that even men of the church, in the name of faith and morals, have sometimes used methods not in keeping with the Gospel in the solemn duty of defending the truth.”

If you detect ambivalence in those words, you are on the road to understanding the difficulty Ratzinger – now Pope Benedict XVI – faces in leading the Catholic Church to properly atone for another stain on its history: the decades of cases of child abuse by priests and cover-ups by their bishops. And while a well-placed Cardinal has publicly speculated that Benedict will deliver a mea culpa in early June, the words of that apology – if that is what it proves to be – will be severely limited by theology, history and the very person and office of the Pope. It is unlikely to satisfy the many members of Benedict’s flock who want a very modern kind of accountability, not just mealymouthed declarations buttressed by arcane religious philosophy. “Someone once told me that if the church survived the Inquisition, it can survive this,” says Olan Horne, 50, an American victim of priestly abuse. “But these are different times. And right now, the modern world is wrapping its head around the Catholic Church in a major way.” (See a photo gallery of the path of Pope Benedict XVI.)

The crisis facing the church is deeply complicated by the fact that in 1980, as Archbishop of Munich, the future Benedict XVI appears to have mismanaged the assignment of an accused pedophile priest under his charge. That revelation – and questions about Ratzinger’s subsequent oversight of cases as a top Vatican official – has been the trigger in turning a rolling series of national scandals into an epic and existential test for the universal church, its leader and its faithful alike. It has blunted Benedict’s ambitious enterprise of re-evangelizing Europe, the old Christendom. Over the past two months, the Pope has led the Holy See’s shift from silence and denial to calls to face the enemies from within the church. What is still missing, however, is any mention of the Holy Father‘s alleged role in the scandal. Can the Pope, the living embodiment of the ancient Gospel and absolute spiritual leader of the world’s 1.2 billion Catholics, publicly atone for his sins and yet preserve the theological impregnability of the papacy?

Without alluding to the crisis, Benedict told his May 26 audience in St. Peter’s Square that “not even the Pope can do what he wants. On the contrary, the Pope is the guardian of obedience to Christ, to his Word.” (See the top 10 religion stories of 2009.)

Benedict now seems to understand the stakes. But Alberto Melloni, a church historian at the University of Modena, says other power brokers in the Vatican think the church can just ride out the storm. “They don’t realize the deep bitterness among the faithful, the isolation of the clergy. We can’t predict where this is going to wind up.” Speaking to TIME, a senior Vatican official foresees immense consequences for the entire church. “History comes down to certain key episodes,” he says. “We’re facing one of those moments now.”

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