The new Pope, Francis the Humble, as he perhaps would like to be known, is an Argentine with a cloudy past. This in itself is not an offense but, rather, is in keeping with a religious institution that has long been marked by secrecy. From the smoke signals with which the papal conclave makes the fact, if not the process, of its decision known to the world to the wide-ranging coverups of sexual abuse involving priests and bishops, the Catholic Church is too often associated in the popular imagination with the darkest kind of institutional opacity.

Some of the cloudiness in Francis’s past has to do with his relative obscurity during the years when he was still known as Jorge Mario Bergoglio, and with the way that the Church operates in even the calmest times. But much of it also has to do with questions about his real role during the country’s anti-Communist terror three decades ago. Officially called the Process of National Reorganization by the military junta that ruled Argentina from 1976 to 1983, the Dirty War, as it is more commonly known, was a comprehensive campaign aimed at the elimination of Communists and others seen as “subversives.” The purge claimed the lives of at least nine thousand people and as many as thirty thousand people, many of them killed in the most gruesome circumstances imaginable. Pregnant women were often held until they gave birth, whereupon they were secretly killed, their babies handed over to childless military families and others close to the regime for adoption. Hundreds of “children of the disappeared” are living today, young people in their early thirties, some of them still unaware that their parents are, in effect, their biological parents’ killers. (Francisco Goldman has written about these children for The New Yorker.)

Many of the victims were held for months in official institutions, where they were repeatedly tortured before being killed, their bodies “disappeared.” Justifying the purge, which was spoken about euphemistically but carried out in secrecy, the Argentine military espoused a brand of anti-Communist ferocity that echoed Franco’s Fascist witch hunt, which had previously devastated Republican Spain—a brand of ferocity that also shared his deeply entrenched ultra-Catholic and anti-Semitic views.

As in Spain during its Civil War, when the Catholic Church openly sided with Franco’s inquisition, and in Rome during the Second World War, when the silence of Pope Pius XII was understood as a tacit admission of Vatican acquiescence with the policies of the Axis, the role of the Argentine Catholic Church in the junta’s anti-Communist campaign was queasily intimate. In official discourses, one of Bergoglio’s predecessors, Archbishop Juan Carlos Aramburu, openly sided with the military’s stated need for a purge, in which freethinking priests and nuns were also killed. For the most part, the Church remained mute in public about what was going on. But some priests were actually directly involved in the repression, by all accounts, with military chaplains going so far as to bless the drugged bodies of suspected guerrillas marked for execution as they were loaded onto military planes, from which they were then hurled to their deaths, unconscious, over the Rio de la Plata.

There have been past accusations, including testimony from a handful of priests and bishops, that the man who is now Pope Francis was complicit, too, if in a more subtle way. He was, in the early years of the Dirty War, the provincial, or superior, of the Society of Jesus in Argentina, at a time when the Jesuits produced some of the more freethinking and socially liberal clerics in Latin America—a number of whom were targeted by military leaders during the era’s repression—and later led a seminary. The key allegation against him is that he pointed out left-leaning priests to the military as dissidents, leaving them exposed, and that he did not defend two kidnapped clerics or ask for their release. He has denied this, and says instead that he protected priests and others—just quietly, in secret.

”Beyond the details, the main thing is that it’s clear that he was not—by a long shot—at the level needed in the dramatic circumstances,” Gabriel Pasquini, an Argentine writer and editor of the online current-affairs magazine El Puercoespín, told me. There were other clergymen—“Catholic and from other religions”—who “did whatever they could to save lives,” Pasquini added. “For someone who aspires to be a bastion of moral values, it doesn’t seem like a great precedent. Never, in the years he headed the Catholic Church in Argentina, did he acknowledge its complicity in the dictatorship, much less ask for forgiveness. Will he do so now, from the Vatican?”

Whatever the truth, Francis the Humble, it would seem, has much to clear up about what he thought, how he behaved, and what he did during his country’s Dirty War. As with the role of the Church he has long served, it remains a mystery.

Photograph: AFP/Getty.