Many in Argentina say allegations are political, attempts by the left to ruin his reputation. Contradictory statements and letters further cloud the issues.
Mercedes Alvarez is among the many here who will never believe that Jorge Mario Bergoglio
, the Argentine chosen to be pope, did anything unsavory during the dark days of this country's "dirty war."
She is aware of the allegations against him. And she has written them off as political gamesmanship.
"What's happening," the homemaker said the day before Pope Francis was inaugurated in Rome last week, "is that our president had been fighting with him, and she is trying to hurt his reputation."
Alvarez, 60, had been praying in a little church in the poor barrio of Bajo Flores, where, 36 years earlier, two Jesuit priests had been snatched by elements of Argentina's right-wing dictatorship who suspected the men of being Marxist guerrillas. They were detained for five months and tortured, then released.
Critics claim the crime occurred with the complicity of Bergoglio, who was a leader of Argentina's Jesuits at the time. They say he gave unmistakable signals to the military that the priests were dangerous leftists and no longer worthy of the church's protection.
But there is much that remains opaque in the matter of the kidnapped Jesuits, as well as a second case from Argentina's period of dictatorship, from 1976 to 1983, in which Bergoglio has been criticized for his response to a query about a dissident's baby, who was apparently stolen by the military junta.
Many here have drawn their own conclusions about the new pope's past, influenced in some cases by the highly partisan politics of modern-day Argentina and unresolved tensions from the dirty war, when as many as 30,000 suspected dissidents were killed or disappeared at the hands of the junta.
The accusations have been around for years, but no court has accused Bergoglio of wrongdoing. He has argued that he lobbied the junta to free the kidnapped priests and quietly worked to hide or protect many other suspected dissidents.
But Bergoglio has had to make that case amid a stream of revelations about other Catholic leaders' collaborations with the junta. In a jailhouse interview last year, the former dictator Jorge Rafael Videla, who is serving a life sentence for human rights abuses, said that some top church officials were aware of the dictatorship's kidnappings and killings of dissidents.
At the same time, many Argentines like Alvarez, who are disposed to think the best of the new pope, suspect that the concerns about him are pure propaganda cooked up by an Argentine left eager to discredit Bergoglio, a social conservative known to clash with Argentina's left-wing president, Cristina Fernandez de Kirchner.
The main chronicler of the priests' kidnap case is investigative journalist Horacio Verbitsky, a former member of a '70s-era leftist guerrilla group who tends to favor the policies of Kirchner's populist government. It was Verbitsky's past and political slant that allowed a Vatican spokesman, shortly after Francis' election, to dismiss the complaints against the new pope as a campaign by "left-wing, anti-clerical elements."
But Verbitsky is also highly regarded for shedding light on some of the worst abuses of the dictatorship. He famously established that security forces drugged dissidents and dropped them from airplanes and helicopters into the Rio de la Plata.
The two kidnapped priests always denied that they were linked to left-wing guerrillas. In the mid-1990s, one of them, Francisco Jalics, described his ordeal in portions of a self-help book he wrote. He and fellow Jesuit Orlando Yorio's work in the 1970s with the poor in Bajo Flores, he wrote, had caused them to be viewed with suspicion by some in the Argentine right.
More specifically, Jalics describes one "person in question" who was spreading rumors that he and Yorio were allied with the guerrillas. The priests confronted this person, whose identity they never revealed, and said that he was putting their lives in danger.
The individual said he would try to convince the military that the pair were not terrorists, according to Jalics. But later, Jalics wrote, he came to the conclusion that this person "hadn't complied with his promise, but rather, on the contrary, had presented a false complaint [about us] to the military." Jalics said the conclusion was based on the declaration of a church official and more than 30 documents that he had discovered. He would later destroy the documents as part of an effort to forgive people who had wronged him.
Verbitsky claims that this "person in question" was Bergoglio, based on a letter that Yorio, the second priest, wrote to a Jesuit authority in 1977. (Verbitsky declined to provide a copy of the letter to The Times.) Verbitsky also claims that Jalics confirmed the story in an interview in 1999.
Bergoglio has strongly denied that he ever gave the men up. In a 2010 biography, he says he pleaded to have them released, visiting twice with Emilio Massera, the navy official who was a key architect of the dirty war, and twice with Videla, the dictator.
On March 15, two days after Bergoglio was chosen as pope, Jalics, who lives in a German monastery, issued a statement saying that he was "unable to comment" on Bergoglio's role in his kidnapping but was "reconciled" with the events after discussing them with Bergoglio.
Verbitsky noted that the statement did not indicate that Jalics thought Bergoglio was innocent. Jalics subsequently issued another statement in which he said "Yorio and I were not given up by Father Bergoglio."
On Thursday, Verbitsky reported Jalics' latest statement but also mentioned, as he has previously, an Argentine Foreign Ministry document he had discovered. The typed document, apparently written by a government official, explains the reasons for denying Jalics a new passport in 1979. It notes that Jalics and Yorio — who died in 2000 — had been detained in 1976 for "suspected guerrilla contact."
That detail was supplied, the document says, by Bergoglio.
In his column, Verbitsky argued that although the 1979 document doesn't prove that Bergoglio had accused the men in 1976, it supports the priests' alleged assertion that Bergoglio was telling them one thing while doing another.
In his biography, Bergoglio acknowledges discussing Jalics' past with the government official. But the cardinal added that the official failed to write down another part of the conversation in which Bergoglio said the men were not linked to the guerrillas.
In another case that has garnered attention, a woman named Estela de la Cuadra has accused Bergoglio of knowing about a junta practice that has become almost as notorious as the dropping of bodies from helicopters: Stealing babies born to dissident mothers in captivity, then placing the babies with families friendly to the dictatorship.
De la Cuadra, in statements to various media, said her pregnant sister and other family members were detained by the military in 1978. Bergoglio, she said, gave her family a note with the name of a priest who could help them find out what happened to them.
According to De la Cuadra, the priest told her father that "there's nothing that can be done, the child has been born, but she is in the hands of a family that will raise her well." Based on this statement, De la Cuadra asserts that Bergoglio too must have known what had happened to the child.
But Bergoglio has insisted that he didn't know about the practice of stealing babies until the dirty war was over.
As Argentina continues the painful process of bringing the secrets of its dirty war to light, it is possible that more details will emerge about the conduct of the man who is now Pope Francis.
But for now, the Vatican's posture is clear: "There has never been a credible accusation against him," church spokesman Father Federico Lombardi said.
D'Alessandro is a special correspondent.