He was in his late teens and still some years away from entering the Jesuit Order. She was in her mid-30s, a revolutionary and a feminist far ahead of her time. They met around 1953 or 1954 in the most unlikely of places – a laboratory where she worked as a pharmaceutical biochemist and he as an apprentice chemical technician. The two could not have been more dissimilar. Yet they cemented a unique friendship that bridged decades as well as deep political and religious chasms.

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The woman was Esther Careaga, a non-believer who, because of her Marxist ideals, disappeared under Argentina’s dictatorship in 1977. The man was Jorge Bergoglio, who became Pope Francis in March this year.

Careaga had arrived in Buenos Aires as a political exile from neighbouring Paraguay a few years before meeting Bergoglio. She had been a fiery socialist orator and the founder of Paraguay’s first feminist movement in the 1940s. “She toured the towns in the countryside of Paraguay pleading for people’s rights in general, but especially the rights of women,” says her daughter Ana María Careaga.

Careaga was one of thousands of people who “disappeared” between 1976 and 1983, a bloody spree that stopped only after Argentina entered into a losing war with Britain in 1982 over the Falkland Islands. Victims were taken to secret camps, tortured and thrown from military planes – drugged but still alive – into the South Atlantic Ocean. It was an unsuccessful tactic because sometimes the bodies washed up on shore days later.

I had frequent contact with Careaga in the months before her abduction on 8 December 1977. I was a young journalist; she was 59. By that time Argentina had fallen behind a wall of silence. Denial had become part of the fabric of society. Torture and death were meted out to those who dared speak out against the murder machine. Clerics and journalists were routinely slaughtered. Most of the press and the clergy clamped their mouths shut.

The newspaper where I worked, the small English-language daily Buenos Aires Herald, was the exception. Its brave British editor, Robert Cox, had decided to make a stand. “It was an honour to scream when everybody else held silence,” says Cox from his retirement home in South Carolina.

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The Herald was visited almost daily by mothers whose sons and daughters had been plucked from their homes by men with machine guns. I found myself derailed into a dark parallel universe where I held hands with the distraught women who came to us – a small newspaper in a foreign language – because nobody else would listen.

Careaga first came to us in July 1977 to report the disappearance of her pregnant 16-year-old daughter Ana María. I was immediately struck by this woman with a steady gaze, who spoke with such soft authority. Unlike the other mothers, who were distraught beyond coherence, she remained in full command of her emotions.

We discovered later that her daughter had been taken to the basement of a police building where more than 1,500 people languished in chains. “They put on cassettes of Hitler speeches to drown out the screams while they tortured us,” Ana María says now. Swastikas abounded there, and Jewish victims were singled out for extra-cruel punishment.

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It was an agony that few returned from. However, whether because her captors took pity on her or because the Herald reported her case, the teenager was released after suffering four months of horror.

Ana María immediately left for Sweden, where she was accepted as a political refugee, but her mother refused to leave. By this time Careaga had joined the “Mothers of Plaza de Mayo” – the mothers who marched every Thursday at the Plaza de Mayo in front of the presidential palace to draw attention to their plight.

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I was surprised when Careaga reappeared at the Herald, and I wondered why she wanted to keep risking her life even after her daughter had been saved. “We have to keep fighting for all the other missing children,” she said.

Shortly before she disappeared, Careaga called Bergoglio, asking him to come and administer the last rites to a dying relative. This struck her old friend as unusual because the Careagas were not a religious family.

Arriving at Careaga’s house, Bergoglio discovered that Careaga was being careful because she didn’t want to reveal the truth over the phone. “My parents had a large library of political books – books on Marxism and philosophy – and she asked him to hold them in safekeeping,” says Ana María. Bravely, Bergoglio did so, even though being found with such literature would have meant death back then.

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Later, Ana María gave birth to a baby girl in Sweden. “We called home only to hear that mother had been kidnapped three days before,” she says. “We thought it was terrible but we never thought …” Her voice trails off. “The last thing you lose is hope.”

Careaga’s daughter eventually returned to Argentina and met with Bergoglio. “I don’t remember any details, you can imagine the condition I was in,” she says. She never found out what happened to her mother’s books. “There was so many more important things to deal with, we never asked.” The rest of the Careaga family did not have the same kind of close relationship with Bergoglio. “He was a personal friend of my mother, it wasn’t a family relationship.”

Later it transpired that Careaga had been taken to the ESMA Navy School of Mechanics – which doubled as a detention centre – where she was brutally tortured, and then flown to her watery death, along with two other Mothers of Plaza de Mayo and two French nuns who helped them.

Bergoglio, ordained Archbishop of Buenos Aires in 1998, was in shock. “I was badly pained, I tried to communicate with some relatives but I couldn’t, they were in hiding,” Bergoglio testified at the ESMA trial in 2010. Asked by a lawyer acting on behalf of the Careaga family if he had spoken to any authorities on her behalf, Bergoglio said, “No authorities, I did what I could.”

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I testified at the same trial on behalf of Careaga and others, including the father of a missing person who was kidnapped on the same day as Careaga. One of the defendants was a Navy captain named Alfredo Astiz, once dubbed the “Blond Angel” because of his light hair and baby face. We learned that he had infiltrated the mothers by pretending to have a missing brother. The mothers adored him. His true identity had come to light during the 1982 Falklands War, when his landing on South Georgia island became the first act of aggression in that war. The mothers were aghast when they saw a picture of him surrendering to British officers.

Astiz was taken to the UK, and although the French government asked prime minister Margaret Thatcher to hold him until they could charge him with the disappearance of the two French nuns, Astiz was repatriated to Argentina. He was finally brought to justice and sentenced to life in 2011.

Before then, in 2005, forensic anthropologists dug up some bodies that had been buried in an unmarked grave after washing ashore in late December 1977 near the beach resort of Santa Teresita, south of Buenos Aires. DNA testing identified them as being the bodies of the mothers that Astiz had kidnapped: Careaga was among them.

Luis Bianco – the son of Ana Bianco, one of the other mothers buried alongside Careaga – was chosen by the victims’ relatives to ask Bergoglio for permission to bury their remains in the gardens of the Church of the Holy Cross, the Irish community church in the city of Buenos Aires, from where they had been kidnapped.

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Bergoglio seemed hesitant. He was puzzled, asking why they should be buried at the church instead of in a cemetery. “I touched his knee,” says Bianco. “I told him that one of the mothers was Careaga.”

Bergoglio shook with emotion.

“Careaga was a good friend and a great woman and I am sure your mother was the same,” he said.

Within a week permission was granted for Careaga and the other mothers to be buried there.

guardian.co.uk © Guardian News and Media 2013