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Despite the apparently exhaustive coverage of the Vatican and its new pope, four fascinating matters remain hanging in the air, some raised, all unresolved.

It has barely been remarked, in the first place, that Pope Francis is not the first leading Roman Catholic accused of being silent in the face of a monstrous regime, in his case that of Argentina's military junta. At issue is nothing less than the relationship of Pope Pius XII to Hitler and the Nazis. Although the subject roils with bitter controversy – one study called Pius "Hitler's Pope" – some matters are clear.

As summarized by Michael Marrus, doyen of Canada's Holocaust scholars, Pius failed to intervene on behalf of Europe's Jews. "Throughout this period the church seldom opposed anti-Jewish persecutions … Despite numerous appeals, the Pope refused to issue explicit denunciations of the murder of Jews or call upon the Nazis directly to stop the killing."

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Pius XII was hardly just another bystander to evil, however. For one of his standing the concept is entirely inadequate; ordinary people can be bystanders, not church leaders. More accurately, he committed the grave sin of omission. Catholics might consider it a mortal sin.

Can the same not be said of Pope Francis during the Dirty War in Argentina, when he was Father Bergoglio, head of the country's influential Jesuit Order? Here is the second nagging issue. A military coup in 1976 produced a fiendish junta that for seven long years tortured, murdered and disappeared some 30,000 Argentines accused of being leftists of some kind or another. As The Globe's Doug Saunders puts it, "priests either sided with the military regime or became targets of its terror." Father Bergoglio was not a target. Although he was not actively complicit in the crimes of the generals, as so many of his fellow priests were, he remained silent about them.

Throughout the 1970s and 1980s, vicious military dictatorships dominated much of Central and South America, promiscuously using terror to intimidate and eliminate opponents on the left. According to former American Ambassador to El Salvador Robert White, himself a Catholic, senior representatives of the Vatican largely supported these brutal regimes. These church leaders, White found, cherished their historic arrangement "of the rich, the military and the church working together," all backed by the United States.

But there were notable exceptions. While in Argentina the Church hierarchy largely sided with the generals, El Salvador was different. There, in a Sunday sermon in March 1980, Archbishop Oscar Romero directly beseeched the extreme right-wing rulers of his tortured country: "In the name of God, in the name of this suffering people whose cries rise to heaven more loudly each day, I implore you, I beg you, I order you in the name of God: stop the repression." He was murdered the next evening.

At the same time in Argentina, Father Bergoglio was largely mute. Perhaps, as he insists, he did intervene on behalf of two former young Jesuit priests kidnapped by the regime; there is much debate on the matter. Curiously enough, he had just dismissed the two men from the Jesuit Order for their work among the poor. In any event, at best they were only two. For the other tens of thousands of the junta's victims, there was only silence, as Bergoglio himself later publicly acknowledged. He and other Argentine bishops begged forgiveness for not doing enough, for, in effect, their sins of omission.

A third issue remains the Church's greatest moral crisis (except perhaps for its wholesale subordination of women): the priests who raped children and the priests who covered up their crimes. As archbishop and cardinal, asserts Ernesto Moreau, an Argentine lawyer who has represented victims of clergy abuse, Bergoglio was "totally silent." According to local rights advocates, Bergoglio failed to take decisive action to protect children, to act against priests who molested children, to extend apologies to the victims of pedophile priests, or to meet with victims and their families – a sad litany. He was, says Moreau, "no different from most of the other bishops in Argentina, or the Vatican itself."

Finally, there is Pope Francis's much-lauded desire for a "poor church". His own modest lifestyle can hardly be denied. Yet it was the very essence of the Argentine dictatorship, as of all the Latin American juntas, that they boldly represented the forces of capital against the poor and the dispossessed. These less privileged were often supported by priests committed to Liberation Theology, a Catholic movement based on Jesus' teachings whose guiding principle was solidarity with, not charity for, the poor. Yet Bergoglio was far more outspoken against Liberation Theology priests than he ever was against the generals.

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Years later, now leader of his church, Cardinal Bergoglio strongly – and with little sign of his celebrated humility – attacked the governments of Nestor and then Cristina Kirchner as he had never remotely criticized the military junta. What were some of the policies he so strongly condemned? The government was finally allowing Argentine women access to birth control and abortion, one step in the process of enabling them to escape from lives of poverty and subordination.

But liberating women is evidently not his way to care about poverty. Nor is standing in solidarity with the poor. How then will he now achieve his church for the poor?

Habemus Papam. We have a new Pope who in every practical aspect embodies the Vatican's enduring priorities. That, we can presume, is why he was chosen.

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