Upon ascending to the papacy today, the newly-anointed Francis addressed the eschatological paranoia that occassioned the resignation of his predecessor, saying that some cardinals had been "seeking the end of the world, but we are still here." But it seemed to be a pun, referencing his native land at the "end of the earth." Among the joyous crowd below in St. Peter's Square were several Argentine flags. Cardinal Jorge Bergoglio is now the first pope from Latin America, something millions around the world had anticipated with hope. But the election of Cardinal Bergoglio deepens growing concerns about the complicity of the Catholic Church in Argentina's "Dirty War" of the 1970s.

Bergoglio, born to Italian immigrants in Buenos Aires 76 years ago, became the top Jesuit official for Argentina in 1973, three years before the military seized power. Democracy was restored in 1983, after a "dirty war" in which perhaps 30,000 were killed or "disappeared"—overwhlemingly peaceful left-wing dissidents. In 1998 he became archbishop of Buenos Aires, and was credited with brokering social dialogue during the 2001 economic crisis in the country. The same year, he became a cardinal. He continued to speak out on behalf of the poor, telling a gathering of Latin American bishops in 2007: "We live in the most unequal part of the world, which has grown the most yet reduced misery the least. The unjust distribution of goods persists, creating a situation of social sin that cries out to Heaven and limits the possibilities of a fuller life for so many of our brothers."

But he remained a vocal defender of the church dogma opposing abortion, same-sex marriage, and contraception. These stances won him public rebukes from President Cristina Fernández de Kirchner, who legalized gay marriage in Argentina, and supports free contraception programs and expansion of abortion rights, at least for rape victims. Fernández compared Bergoglio's stances to "medieval times and the Inquisition."

And, following the trajectory of Pope John Paul II, Bergoglio's concern with the poor seems to have emerged only after the end of the Cold War, when such preoccupations were no longer seen only as fodder for leftist subversion. Under Bergoglio's leadership, Argentina's bishops issued a collective apology in 2012 for the church's failure to protect its flock during the Dirty War. But the statement was assailed for seeming to cast equal blame for the era's violence on the military regime and its opponents—as well as for being years too late.    

Bergoglio faced a growing controversy over his apparent collaboration with the dictatorship when it was in power. While some clergy in those years were moving into "base communities" in the country's barrios and peasant lands, taking up activism in solidarity with the poor, Bergoglio ordered that Jesuits continue to staff parishes—and serve as military chaplains.

Bergoglio twice invoked his right under Argentine law to refuse to testify in cases concerning the Dirty War. When he finally did testify before Oral Tribunal No. 5 in 2010, rights activists charged that he was evasive. "When someone is reluctant, he is lying, he is hiding the truth," said attorney and former lawmaker Luis Zamora, who brought the case demanding a judicial investigation into torture at the infamous Naval Mechanics School (ESMA).

The 2010 case concerned the torture of two of Bergoglio's Jesuit priests—Orlando Yorio and Francisco Jalics (rendered Yanis in some accounts)—who were abducted in 1976 from the barrio where they worked with the poor, and held for five months at the ESMA. Yorio accused Bergoglio of betraying them into the hands of the torturers by declining to tell the junta that he supported their work. Jalics moved into seclusion in a German monastery after his release. Bergoglio told Francesca Ambrogetti and Sergio Rubín, the writers of his authorized biography, El Jesuita, released the same year as his testimony in the case, that he took behind-the-scenes action to save the abducted priests—including persuading dictator Jorge Videla's family priest to call in sick so that he could say Mass in the junta leader's home and privately appeal for mercy.

The 2008 case in which Bergoglio declined to testify—above the protests of the Grandmothers of the Plaza de Mayo rights group—concerned the theft of the babies of the disappeared. After the disappearance of her pregnant daughter in 1977, the founder of the grandmothers' group, Alicia "Licha" de la Cuadra, even appealed to the leader of the Jesuit order in Rome, who urged Bergoglio to help. Bergoglio then assigned a monsignor to the case. Months later, the monsignor turned over a written note from a colonel asserting that Licha's daughter had given birth in captivity—but the baby girl had been given to a family "too important" for the adoption to be reversed. Bergoglio did comment on the controversy in his 2010 testimony—two years after Licha died at the age of 93. He then said he didn't know of any stolen babies until after the dictatorship ended—despite the letter from the colonel, since revealed in the press.

"Bergoglio has a very cowardly attitude when it comes to something so terrible as the theft of babies," Licha's surviving sister, Estela de la Cuadra, told the Associated Press upon the Cardinal's selection as pope. "He says he didn't know anything about it until 1985. He doesn't face this reality and it doesn't bother him. The question is how to save his name, save himself. But he can't keep these allegations from reaching the public. The people know how he is."  

But the most damning claims came from journalist Horacio Verbitsky, in his 2005 book about Church complicity in the Dirty War, El Silencio. He claims that in 1979, Bergoglio conspired to hide the disappeared detainees at the ESMA from a visiting delegation of the Inter-American Human Rights Commission. According to Verbitsky, Bergoglio allowed the detainees to be temporarily sequestered at his vacation home on an island in the Río Plata, called El Silencio. (National Catholic Reporter, AP, NYT, Consortium News, La Prensa, Nicaragua, March 14; El País, Madrid, El Periodico, Barcelona, March 13; El Díá, La Plata, May 2, 2011; Ámbito, Buenos Aires,  Nov. 8, 2010)