The election of Pope Francis has thrown a spotlight on his conduct as a priest under Argentina's military dictatorship in the late 70s and early 80s, and in particular at what point he found out about one of the country's most shameful episodes.

Nearly a month has passed since the Roman Catholic Church elected its first leader from Latin America and the international media has been treated to a whirlwind blitz of eye-catching tales and images.

Pope Francis appears to be what Argentinians would say is "campechano" - approachable, "matey", even.

He has washed and kissed the feet of women and Muslims, inscribed his autograph on plaster casts of injured pilgrims and has even telephoned his old Buenos Aires news vendor to cancel his newspaper order. And perhaps most eye-catchingly of all, he has said he wants to see as a priority "a poor Church for the poor".

It has all been perceived as a breath of fresh air. The stuffy papacy, which resembled a mediaeval monarchy, some say, is now gone.

But lurking beneath the surface are pressing concerns that threaten to dog Jorge Mario Bergoglio from his time as Jesuit superior and cardinal of the Roman Catholic Church in Argentina.

Within 24 hours of the white smoke from the Sistine Chapel, allegations emerged that he withdrew protection from two of his fellow Jesuits during the early years of the brutal military dictatorship of 1976 to 1983, which resulted in their captivity and torture.

The Vatican acted swiftly to deny the claims. The remaining surviving priest, Fr Francisco Jalics, issued an initial statement saying he was "reconciled with these events". The words appeared ambiguous. Might he be saying he was betrayed but has now forgiven the Pope for his betrayal?

A week later, a more robust statement was issued from his secluded monastery in southern Germany, saying that it was "wrong to assert that our capture took place at the initiative of Father Bergoglio". Any suggestion of a smoking gun appeared to have been extinguished.

But can Bergoglio's efforts to be a witness for justice during the dark days of the military regime compare with those of Oscar Romero, the archbishop from El Salvador, whose uncompromising criticism of government death squads and oppression of the poor led to him being assassinated in 1980 as he celebrated Mass?

"Bergoglio was not a Romero. Very few people were like that," says Ivan Petrella, religious affairs commentator at think tank Fundacion Pensar in his Buenos Aires office.

But if Romero scored 10 on a 10-point scale for his courageous stand, how had the current Pope fared? "I´d say 7.5," says Petrella. "Allegations against him have no basis in evidence."

But there is another story that demands answers - the supremely toxic affair of "disappeared" pregnant women, who gave birth to their children while being held in detention centres. Most of the mothers were murdered and their children handed on to "deserving" couples who were well connected with the brutal military junta.

This is very much a live political issue. A number of the children have discovered the painful truth about their past, while hundreds more still remain blissfully ignorant of their parentage. The campaigning grandmothers assert that many priests and nuns were complicit in what happened and are still at large in society. They show no sign of letting the matter rest.

At first sight, this is not an issue that should threaten Pope Francis. In 2010 he was asked in front of a state tribunal when he first knew of the cases of children being taken from their mothers.

Radio 4's The Report has managed to track down the audio from his testimony in which he says, initially: "Recently, about 10 years ago." Then he pauses, and corrects himself. "No, it must have been around the time of the military junta trial." The mid-1980s, in other words.

Image caption Estela de la Cuadra lost five members of her family during the 'dirty war'

However, this is not accepted by Estela de la Cuadra who tells a spine-chilling tale about one mother and child who disappeared.

Estela's five-month pregnant sister, Elena, was seized in February 1977 and gave birth to a daughter, Ana, in July of that year in a local detention centre station where she was being held. Estela's father, Roberto, sought the help of Fr Bergoglio in trying to find out what happened to his daughter.

Estela showed me a letter dated 28 October 1977, signed by Fr Bergoglio, then a Jesuit provincial father. He was writing to a local area bishop on behalf of Mr de la Cuadra. The letter, which Estela showed me, reads as follows:

"I am going to the trouble of introducing Mr Roberto Luis de la Cuadra, with whom I had a conversation…. He will explain to you what it is about."

Estela is adamant that the letter shows that the Pope withheld the truth in court in 2010, but the text shows no such thing. There is no explicit mention of "missing children," just a general reference to a matter of concern. The letter shows Pope Francis using his good offices to help and build bridges.

However, a year after the 2010 court hearing, there was a further inquiry, this time specifically into the cases of "los ninos desaparecidos" (the children who disappeared). This time, lawyers were able to pinpoint the de la Cuadra case in their questions to the then Cardinal Bergoglio.

The Report has obtained a transcript of his responses. He tables answers to 33 questions in which he says, in answer to No 13, "[Roberto de la Cuadra] told me that his daughter had been kidnapped. I don´t recall him telling me if his daughter was pregnant." In a later answer (No 19) , he says he only came to hear about the birth of the child in captivity many years later through media reports.

All of which may well be the case but these answers prompt further questions.

Image caption Letter dated 1977 from the then Fr Bergoglio regarding Elena De La Cuadra

The stories of missing children were not kept under wraps in Argentina during military rule. Estela showed me French, Brazilian and Canadian press reports from 1979, which carried out detailed investigations into the phenomenon. There were reports in the English-speaking Buenos Aires Herald, a publication which incurred the wrath of the ruling military junta.

Argentina's dictatorship 1976: Military junta under General Jorge Videla seizes power - thousands of political opponents are rounded up and killed in what becomes known as "the dirty war"

1982: Videla's successor, General Leopoldo Galtieri, orders invasion of British-held Falkland Islands - more than 700 Argentine soldiers killed in its unsuccessful defence

1983: Civilian rule returns to Argentina, and investigations into human rights abuses begin

2010: Videla is sentenced to life imprisonment for murders during his term in office

2012: Videla sentenced to 50 years for overseeing systematic theft of the babies of political prisoners

Moreover, there is TV archive footage of the campaigning mothers and grandmothers from 1979, in silent procession in the Plaza de Mayo, in the very heart of the city of Buenos Aires, holding up pictures of their missing loved ones.

They spoke out to foreign news crews about their families, courageous acts which at one stage ended up with General Galtieri´s regime firing rubber bullets at the women to try and evict them from the square.

The Society of Jesus is an international order with nearly 20,000 priests worldwide. News is circulated widely among the various provinces so if Father Bergoglio did not learn about any of this until 1985, as he said under oath in court, it appears he was leading quite an insulated existence.

In 1998, Bergoglio was made archbishop of Buenos Aires, effectively the titular head of the Argentine Catholic Church and in 2001 he was made a cardinal.

Ten years later, in the 2011 court hearing into the cases of missing children, he was asked if the Church had ever held or was, at the time, currently holding, a commission of enquiry into these matters.

His written reply reads as follows: "I don't know if the hierarchy had such a body during the military dictatorship. It's possible that a lay group of the faithful of a religious congregation set something like that up or is currently doing it. I don't know."

Image caption The fate of the 'desaparecidos' remains a political issue in Argentina

We asked the Pope´s press spokesman, Father Federico Lombardi, to comment on the issues raised by the story of Estela´s sister and her missing niece, Ana. He replied: "As you know, the case of the de la Cuadra family has already been raised many times and Cardinal Bergoglio has given his answers. I have nothing more to add."

Estela, who lost five of her relatives during the so-called "dirty war" and ended up fleeing the country as a UN refugee, is not giving up her fight: "We have asked Bergoglio to open up the Church archives so we can find out what really happened."

She carries on waiting.

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