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The Vatican has also been on the defensive with the media. It's denounced the New York Times, among others, for pursuing stories that suggest church officials, including the pope, failed to act against priests credibly accused of abuse. But no paper has covered sexual abuse within the church longer than the National Catholic Reporter.
Now, as NPR's David Folkenflik reports, the paper has published an editorial questioning the pope's credibility.
DAVID FOLKENFLIK: Its a small independent, not-for-profit newspaper based in Kansas City, Missouri, with just eight full-time news staffers and 34,000 subscribers. Joe Feuerherd is the paper's publisher.
Mr. JOE FEUERHERD (Publisher, National Catholic Reporter): NCR was founded about 45 years ago to report on the news of the church, like a good local or good city newspaper covers the news of its municipality.
FOLKENFLIK: From its founding, the National Catholic Reporter embraced a liberalism inspired by the reforms of the Vatican II Council. Kenneth Woodward contributed articles in the early days. He went on to be the longtime religion editor of Newsweek magazine.
Mr. KENNETH WOODWARD (Former Religion Editor, Newsweek Magazine): This was a novelty. Most of the papers were owned by bishops and they were house organs. These people did independent reporting, and they did it right from the start with high journalistic standards. And it was pretty exciting.
FOLKENFLIK: Its best-known reporter may be the ubiquitous John Allen Jr., a respected authority on Vatican doctrine and politics, who's become the paper's public face. But the National Catholic Reporter assigns correspondents and freelancers to travel across the country and across the world to chronicle good deeds and success stories, as well as the tensions within the church. One story has always been different.
Mr. THOMAS FOX (Editor, National Catholic Reporter): Beginning in 1985, we started to see reports of victims of clergy abuse whose parents were eventually going to court to take on the church after approaching bishops and priests and not getting any satisfaction from their complaints.
FOLKENFLIK: Thomas Fox is the paper's top editor. He says a pattern soon emerged.
Mr. FOX: The two parts of this, one was the clergy abuse and the second was the cover-up of the local bishop. And that usually went with the bishop denying that the abuse ever took place, and then often turning on the victim, saying that that person was just making it up.
FOLKENFLIK: Fox says reporters often found that priests were shuffled to other parishes, and complaints of abuse would recur. Even back then, the National Catholic Reporter called for full accountability from the church. The coverage created a backlash.
Mr. FOX: We were getting letters from bishops. We were getting letters from priests and letters to the editor, who were saying at that time that we were really destroying the church. And it was a very, very lonely and very difficult period for us.
FOLKENFLIK: Now, after episodic eruptions, the issue has once again surfaced with a vengeance in Ireland, Germany, the U.S. and Italy. And it has reached inside the Vatican itself.
Last week, the National Catholic Reporter published a new editorial that starts tough and only gets tougher.
Mr. FEUERHERD: The focus now is on Benedict. What did he know? When did he know it? How did he act once he knew?
FOLKENFLIK: That's publisher Joe Feuerherd reading the editorial he wrote with Tom Fox.
Mr. FEUERHERD: The strategies employed so far - taking the legal path, obscuring the truth - have failed miserably. We now have the largest institutional crisis in centuries, possibly in church history. It is time, past time really, for direct answers to difficult questions. It is time to tell the truth.
FOLKENFLIK: I asked Fox if he and Feuerherd were aware of the weight of their words in that most recent editorial. Here's part of our interview.
And yet the language reminds me of Watergate. What did he know? When did he know it? How did he act once he knew, right? I mean, it's talking about the credibility, the ability of the pope to lead the church, right?
Mr. FOX: I think thats correct and these are not just questions that we're asking. These are questions that Catholics around the world are asking.
FOLKENFLIK: This time around, the Catholic journalists, with dual mandates of faith and truth telling, say theyve received few outraged protests for their coverage. Instead, Fox says, they get letters from people who say they have also been abused. And they ask, can you tell our story as well?
David Folkenflik, NPR News.