Pope Francis addresses a synodal meeting at the Vatican in early October.Tony Gentile / Reuters

VATICAN CITY—When the sex-abuse crisis in the Catholic Church flared up in 2002, in the waning days of Pope John Paul II, with allegations of a pattern of abuse by priests and cover-ups in the Archdiocese of Boston, it was often dismissed at the Vatican as “a Boston problem.” When it flared up again in 2010, under Pope Benedict XVI, the atmosphere at the Vatican was a mix of stonewalling and open hostility. Back then, there were new allegations in the United States, as well as new questions about how Benedict had handled some cases of predator priests in his previous roles as head of the Vatican’s doctrinal office and as a cardinal and bishop in his native Germany. Some officials decried calumnious attacks against the Holy Father. The issue was seen in terms of sin and forgiveness more than crime and punishment.

From inside the high walls of Vatican City State, I had the sense, in the years I covered the Vatican for The New York Times, that for many prelates the victims were an abstraction, far away in local dioceses, whereas the calls for more accountability by bishops—and certainly questions about what the pope knew when and what he did about it—were seen as attacks. The hierarchy circled the wagons. There was talk of Masonic plots, even Jewish conspiracies.

When the sex-abuse crisis in the Catholic Church flared up again this August, under Pope Francis, the tone from the Vatican was far less hostile toward the outside world—some officials even spoke of how the Church had been “humbled” and “humiliated” by the crisis. But the atmosphere inside the Vatican is far more divided, and even toxic. Today—when so many American dioceses have filed for bankruptcy after paying settlements to victims, when a scathing grand-jury report released this summer in Pennsylvania found that priests had abused 1,000 children there over decades, when a similar report released in Germany last month found priests had abused 3,600 children over decades, when Ireland has turned away from the Church after scores of revelations of horrific abuse, and after the resignation this year of bishops in Chile in a long-running abuse crisis in that country—there’s a growing awareness that the sex-abuse crisis is of the Church’s own making, not the press’s. There’s also an awareness that it has rocked the institution’s moral authority to the core among many faithful, and that it must urgently and dramatically be repaired to restore trust in the centuries-old institution.

What concrete steps the Vatican will take to fix it, however, are not at all yet clear. The latest sign of extreme cognitive dissonance from the top came on Friday, when Francis accepted the resignation of Cardinal Donald Wuerl of Washington, D.C., but also praised Wuerl for his “nobility” in having chosen not to defend himself by justifying his past actions. Wuerl had been named in the Pennsylvania report more than 200 times, with accounts that he mishandled accusations against predator priests when he was the archbishop of Pittsburgh.

The pope is known to be fiercely, even blindly, loyal to those he finds simpatico, both personally and theologically. He faced a torrent of protests after he defended a Chilean bishop accused of covering up abuse by a notorious priest, Father Fernando Karadima—until Francis requested an investigation that changed his mind, at which point he defrocked Karadima, a turning point in the pope’s handling of the crisis. On Saturday, the pope defrocked two Chilean bishops. Still, if Francis wanted to send a message that bishops should be held accountable, then praising Wuerl and asking him to stay on until his successor has been chosen—as well as keeping him on a powerful Vatican congregation that chooses future bishops—was not a move entirely commensurate with that goal. “You have sufficient elements to ‘justify’ your actions and distinguish between what it means to cover up crimes or not to deal with problems, and to commit some mistakes,” Francis wrote Wuerl in a letter made public by the Archdiocese of Washington. “However, your nobility has led you not to choose that way of defense. Of this, I am proud and thank you.”

This message will no doubt infuriate many sex-abuse victims. So why is the pope sounding so equivocal? In part, it’s because this time the sex-abuse crisis came back into the headlines in August under some unusual circumstances, when a renegade archbishop with a dossier of information, a grudge to bear against Francis for demoting him, and access to a variety of activist Catholic websites published an open letter calling on Francis to resign. The archbishop, Carlo Maria Viganò, alleged that Francis had lifted sanctions placed by Benedict against former Cardinal Theodore McCarrick, an archbishop emeritus of Washington, D.C. The pope had stripped McCarrick of his title in July, following reports that McCarrick had had decades of dalliances with seminarians and had abused an underage altar boy.

The Viganò letter not only conflated the broader sex-abuse crisis with the individual sad case of McCarrick—it also became a salvo in another crisis for Francis’s papacy, one in which Viganò and other traditionalist forces inside the Vatican are seeking to undermine and weaken a pope with whom they profoundly disagree on theological grounds. (They believe the pope has sowed confusion with offhand remarks that indicate an openness to showing more mercy toward gay people—the pope’s now-famous “Who am I to judge?” remark—as well as toward divorcees who seek to receive the sacraments or remarry in the Church.)

This conflation of the sex-abuse crisis and the McCarrick case has seemingly made it difficult for Francis to respond to the former without falling into the quicksand of palace intrigue and brazen backstabbing that were the substance of Viganò’s letter, in which the archbishop also outed a number of Vatican officials as gay and claimed the Church needed to be cleansed of them. When Francis in his letter praised Wuerl for acting “to stimulate” the “unity and mission of the Church,” above “every kind of sterile division sown by the father of lies who, trying to hurt the shepherd, wants nothing more than that the sheep be dispersed,” this seemed to be a reference to the Viganò letter.

For weeks, Francis chose not to respond to Viganò’s claims that Francis knew McCarrick had been sanctioned by Benedict, beyond Francis repeatedly calling efforts to create divisions within the Church, such as the Viganò letter, the work of the devil. Then, last weekend, the Vatican responded with a one-two punch. It said it would examine its archives to find out what was known about McCarrick when, and Cardinal Marc Ouellet, the prefect of the Congregation for Bishops on which Wuerl serves, published a fierce letter with the approval of the pope. He refuted key points of Viganò’s letter, such as that Francis had lifted sanctions placed on McCarrick by Benedict, but indicated that the Vatican had informally urged McCarrick, who retired in 2006, not to travel or appear in public “so as not to provoke more hearsay about him.” Above all, Ouellet wrote, “I find it absolutely abhorrent that you have exploited the clamorous scandal of sexual abuse in the United States to inflict an outrageous and undeserved blow against the moral authority of your superior.”

“The Viganò affair is the tip of an iceberg,” Sandro Magister, a veteran Vatican reporter for the blog Il Settimo Cielo, told me. “Most of it is below the surface. It raises serious questions that are causing divisions at the highest levels of the Church.” Those divisions, in his view, have to do with differences over Francis’s approach to management, theology, and homosexuality. That may be the case. But in many ways, the Viganò letter and the Vatican’s response underscore one of the biggest challenges facing the Church’s handling of the sex-abuse crisis: the often yawning divide between the world viewed from the Vatican and the Vatican viewed from the world. It’s hard to imagine that most parishioners are following the Viganò case, but at the same time, have the officials inside Francis’s Vatican begun to understand that the sex-abuse crisis is a true crisis—and that calls for bishop accountability are not comparable to the persecutions of Christians under the Emperor Diocletian?

“I think there’s a general recognition that it’s not just an English-speaking problem, and it never really was,” Bishop Frank J. Caggiano of Bridgeport, Connecticut, told me last week in Rome, where he is one of six bishops from the U.S. attending an annual synod of bishops at the Vatican this month. The synod’s theme is “young people, the faith, and vocational discernment.” “I think we’re beyond all that,” Caggiano said. “I think the narrative has broadened now. Now there are calls for transparency. We want to know the full extent of this evil. Which means, for example, even very long-past historical cases.”

In an address before Francis and the synod assembly, Caggiano called on the gathering to address the sex-abuse crisis. “It is both a crime and a sin that has undermined the confidence and trust that young people must have in the Church’s leaders and the Church as an institution, so that they may again trust their priests and bishops to exercise true spiritual fatherhood, serve as adult figures in their lives and as authentic mentors of faith,” he said. The Archdiocese of Bridgeport just appointed a layperson, a former judge who is not Catholic, to review its records and issue a report.

Caggiano was not the only prelate to use the word crime in this context—another major shift since 2010. In an October 5 conference at the Jesuit-run Gregorian University in Rome, which has set up a master’s program in the protection of minors, Cardinal Reinhard Marx of Munich and Freising used the term when he spoke of what he had learned from the report published last month uncovering abuse in Germany. (The issue has come to the fore in Germany, where last month Der Spiegel had a cover story about what it said was Francis’s troubled record on the issue as a bishop and cardinal in his native Argentina.) Marx, who has been nicknamed “the Panzer Cardinal” for his insistence that the Vatican tackle this crisis, was unsparing. “Abuse is a crime. In any civilized society, it is normally obvious how to handle crimes. They must be investigated and dealt with,” he said. Marx spoke about the excuses made in the past by clergy to explain their lack of action. “The epitome of self-deception by those responsible was using theological argumentation as an excuse for doing nothing about abuse,” he said. “You know the terms: reconciliation, mercy, benevolence, and clemency to override such considerations as repentance, atonement, and legal consequences, and negate any such actions.”

The Vatican official who probably knows most about the sex-abuse crisis—what the Vatican has done, hasn’t done, and what he thinks it should do—is Archbishop Charles Scicluna, who for a decade was the Vatican’s sex-crimes investigator and is now the archbishop of his native Malta. At a news conference at the Vatican last week, he said the synod was “an important moment” for the Church to address the issue, and that it had been moving to hear a mea culpa from Archbishop Anthony Fisher of Sydney apologizing to young people for the failures of the Church. The abuse crisis is “a big humiliation and it’s going to make us humble,” he said. “What do I say to people who don’t go to church ‘because you say one thing and you do the opposite, shame on you’? I think we need to say, ‘Yes, you’re right, shame on us.’”

Scicluna added, “We need to go to the grass roots to empower people to disclose abuse but also to raise the threshold of accountability.” He also said how important it was to respect civil justice “because the answers don’t have to come only from inside the Church as to who is fit for his office,” and he noted that in Malta he relies on lay experts to help investigate cases and send recommendations. “I need to talk to experts, I can’t just talk to my own conscience,” he said.

These words were important. But what of concrete action? In 2013, Francis set up the Pontifical Commission for the Protection of Minors to tackle abuse. Last year, one of its most prominent members, Marie Collins, an abuse survivor from Ireland, quit in frustration. In a damning letter, she accused Vatican officials of starving the commission of resources and attention, and failing to act on its recommendations—including a tribunal that would hold bishops accountable. The pope approved the creation of such a tribunal, but the then-head of the Vatican’s doctrinal office, Cardinal Gerhard Müller, blocked it on unspecified legal grounds. (Francis subsequently replaced Müller in the post and Müller has become a vocal critic of Francis.)

Francis has often attributed the sex-abuse problem to “clericalism”—a kind of careerism among prelates, or a tendency to look inward and protect the institution, rather than to look outward toward the world. Father Thomas Rosica, who directs a Catholic television network out of Toronto and has assisted the Vatican with communications in recent years, has written that Francis uses “clericalism” to mean a kind of “ecclesiastical narcissism,” as well as a “club mentality and a corrupt system of cronyism.”

This is certainly a challenge for Francis if he’s trying to reform the Vatican, where for centuries power-hungry Italians have been maneuvering and outmaneuvering outsiders like Francis, who had never worked in the Vatican before becoming pope. But does the pope understand the scope of the sex-abuse problem, and will he take measures to tackle it?

The first day of the synod, I asked a veteran Vatican reporter, an Italian, how he thought Francis had been handling the abuse crisis, as well as the Viganò-letter crisis. He said he didn’t think Francis was blind, but the problem was so vast that it was hard to know where to begin. “Look,” my colleague said, as the television monitors on the press-room wall showed the pope greeting row upon row of bishops and other synod attendees in Saint Peter’s Square, “if Francis dismissed everyone in the Vatican who was compromised on this issue, it would be him and Parolin sitting around playing cards.” He was referring to Cardinal Pietro Parolin, the Vatican secretary of state.

My colleague was absolutely right. Francis’s handling, or mishandling, of the scandal in Chile shows him at his worst and best, as someone who stands by those to whom he’s loyal but who, when faced with new evidence, is also willing to change his mind. The Vatican will have made progress on sex abuse when the words coming from prelates around the world—like those of Bishop Caggiano, Cardinal Marx, and Archbishop Scicluna—translate into decisive action from the top. After the Viganò letter landed, Francis called a meeting of bishops next February to address the abuse crisis, and perhaps to pave the way for such action. How the pope handles this crisis—whether he manages to bridge the perception gap between the Vatican and the world—will be a crucial test for his papacy.

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