Father Jorge Mario Bergoglio was 39 years old when Argentina’s military junta seized power in March 1976.

The seven years that followed were a time of infernal darkness in his country. Union leaders, students, journalists and other left-wing activists were rounded up on the mere suspicion of “subversion.” Many were tortured and raped, or tossed alive from military airplanes into the mouth of the Plata River. As many as 30,000 Argentines were murdered or went missing.

As the young leader of the country’s Jesuit order, Bergoglio was aware of the atrocities that were being carried out and worked quietly to save victims, according to people who knew him then. But Bergoglio, like many other clerics at the time, remained publicly silent about the abuse and did not openly confront the military leaders.

“He was anguished,” said Alicia Oliveira, a former federal judge and top human rights official in Argentina, who said that she has known Bergoglio for more than four decades. The two met frequently during the “Dirty War” years, but when Oliveira urged him to speak out, “he said he couldn’t. That it wasn’t an easy thing to do,” she said.

Exactly what Bergoglio did — and didn’t do — during the years of the dictatorship is now the focus of intense scrutiny since his ascendancy to Pope Francis, with the Vatican pushing back forcefully against allegations that Bergoglio failed to protect two left-leaning priests in his Jesuit order, Orlando Yorio and Francisco Jalics, who were kidnapped by soldiers in 1976 and imprisoned for five months.

On Friday, the Vatican denounced the allegations as “slanderous and defamatory.” The Vatican spokesman, Federico Lombardi, said the accusations against Bergoglio were the work of “anti-clerical left-wing elements to attack the church [that] must be decisively rejected.”

In October, Argentina’s bishops issued a collective apology for the church’s failures to protect victims during the dictatorship, but the statement seemed to place equal blame for the violence on the military government and its leftist opponents.

Bergoglio did not speak publicly about his role during the dictatorship until 2010, when he told an interviewer that he hid and protected several persecution victims at the Jesuit seminary, but could not say how many. He also recounted helping a young man who shared his likeness to escape across the Brazil border, giving the man his identification card and dressing him up in clerical vestments as a ruse. “It saved his life,” Bergoglio said.

In 2010, Bergoglio declined to appear in court after being called to testify as a witness in the trial of 18 military officials who ran the Naval Mechanics School, where detainees were often taken and tortured. It was the same detention center where Yorio and Jalics were taken after their arrest on suspicion of associating with left-wing guerrillas in the Buenos Aires slums where they worked under Bergoglio.

Citing “clerical immunity” granted by Argentine law, Bergoglio insisted on giving testimony in his church offices and told investigators that he personally intervened with the country’s military rulers on behalf of the young priests. A transcript of his four-hour interview has been published online by Argentine rights groups, and attorneys close to the case verify its accuracy.

At one point, Bergoglio said he met privately with military commanders, including coup leader Emilio Massera to inquire about the missing Jesuits. “Look Massera: I want them to appear,” Bergoglio said he told him in a tense encounter before abruptly walking out of the room.

Yorio and Jalics were eventually freed, dumped off in a field after five months, half-naked and drugged.

Yorio later blamed Bergoglio for the imprisonment. In a 1999 interview with a respected Argentine journalist, he was quoted as saying, “I have no reason to believe [Bergoglio] did anything to free us, in fact just the opposite,” suggesting his superior had lifted his protection on the men as a punishment for their political views.

Yorio died in 2000.

Jalics, the other priest, had been silent about Bergoglio until Friday, when he issued a statement saying he had spoken with Bergoglio years later and the two Jesuits embraced “solemnly.”

“I cannot make a statement about the role of Father Bergoglio in these events,” he said. “I am reconciled to the events and consider the matter to be closed.”

Government targets

Throughout Latin America during the Cold War, priests who were adherents of the Marxist-inspired “liberation theology” movement were often targeted by right-wing governments. Other clerics went to great lengths to protect victims of abuse and their families, and denounce abuses.

But Argentina’s church leaders did not confront the country’s military rulers with anything approaching the public fervor of fellow clerics facing other dictatorships, as in Chile or El Salvador, where Oscar Romero, the archbishop of San Salvador, was assassinated in 1980.

Some of Argentina’s best-known rights advocates, the mothers and grandmothers of disappearance victims, have been outspokenly critical in recent days of Bergoglio’s handling of another case involving a child born to a mother inside a military detention facility in 1977.

The mother’s family appealed to Jesuits in Rome for help, and they asked Bergoglio to intervene. But the child was never returned to the family, becoming one of hundreds of babies allegedly stolen and illegally adopted by military officials after their parents were killed.

Bergoglio later said in a 2011 written testimony related to the case that he was unaware of the practice at the time.

“He did nothing to help us during those years,” said Rosa Tarlovsky de Roisinblit, 92, a member of the Grandmothers of the Plaza de Mayo whose daughter Patricia disappeared in 1978. “But he was only one of many,” she said.

‘Ongoing debate’

Tex Harris, a U.S. Foreign Service officer who was based in Buenos Aires during the dictatorship and worked to document disappearance cases, said that while many in Argentina knew what the military was doing, few had any idea of the scope of the “state terrorism.”

“In every secular and religious organization in Argentina, there was ongoing debate in this period as to what was the most effective way to bring back the disappeared,” he said. “Should they work quietly or confront the government?”

The goal, Harris said, was to get the victims — often young adults and teenagers — back from military custody. “They were convinced that they were being held in detention facilities.” But many never came back. “Most ended up in mass graves,” he said.

The criticism of Bergoglio for not doing enough has prompted several prominent Argentine rights activists, including Nobel Peace Prize winner Adolfo Perez Esquivel, to come to his defense in recent days.

“There were some priests and bishops that helped the dictatorship, and others who spoke out and died because of it. But Bergoglio wasn’t a collaborator,” said Graciela Fernandez Meijide, a politician and prominent human rights investigator whose 16-year-old son vanished after being snatched from his bed by soldiers in the middle of the night.

It was an era during which the clerical vestments offered little protection, she said, and prominent members of the clergy were targeted. “And even if he wanted to denounce the government, who would he have turned to?” she said.

Julie Tate in Washington, Jason Horowitz in Rome and Michael Birnbaum in Berlin contributed to this report.