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From NPR News, this is ALL THINGS CONSIDERED. I'm Melissa Block.

A federal grand jury is investigating the Catholic Archdiocese of Los Angeles over its handling of sex abuse by priests. The church has settled with more than 500 victims but serious questions remain. An NPR investigation reveals that Cardinal Roger Mahony, along with his top officials and even his review board, failed to act when presented with pedophile priests. NPR's Barbara Bradley Hagerty examines the case of one the most notorious abusers: Father Michael Baker.

BARBARA HAGERTY: In 1986, Cardinal Mahony found out that Father Michael Baker had been abusing boys from an impeccable source: the priest himself. Father Baker told Mahony that he molested two boys, beginning in 1978. Tod Tamberg, the spokesman for the archdiocese, says Mahony responded the way everyone did back then.

Mr. TOD TAMBERG (Spokesman, Catholic Archdiocese of Los Angeles): Cardinal Mahony decided to handle it pastorally and thought that the thing to do would be to make sure that Michael Baker got the kind of treatment that he needed and the kind of help he needed so that he could make himself whole again.

HAGERTY: After six months of treatment, Baker was put in restricted ministry. He was not supposed to have contact with children and he was supposed to be monitored by other priests. But over the next 14 years, Baker was moved to nine different parishes, several of which had elementary schools adjacent to the rectory.

That was clearly inadequate, says plaintiffs' attorney Lynne Cadigan.

Ms. LYNNE CADIGAN (Attorney): Why is it the church's job to monitor them? Why doesn't he be monitored in jail or prison like any other person?

HAGERTY: Cadigan represents two brothers who say Baker began molesting them in 1984, when they were five and seven years old. The priest babysat for the boys, and when the family moved to Mexico, Baker visited them, took them on trips, helped arrange for them to move to Tucson. And all that time he was theoretically being monitored by the archdiocese.

Ms. CADIGAN: Baker obviously wasn't monitored. He paid for everything. He bought them a house with church money, and he supported their mother.

HAGERTY: Cardinal Mahony did set up stronger policies to stop abuse. For example, creating the Sexual Abuse Advisory Board in 1994. The four priests and four Catholic laypersons on the board were supposed to be advocates for the victims.

Richard Byrne, a retired judge, has served on the board since the beginning. He says the vicar for clergy, who oversaw all the priests in the archdiocese, would present each case as a hypothetical with no names.

Mr. RICHARD BYRNE (Retired Judge): And then we would discuss that. This was purely advisory to the vicar. We assumed that the vicar then spoke to the cardinal.

HAGERTY: Byrne says the board didn't have authority to make recommendations, nor could it conduct investigations. Those were done by the archdiocese.

Mr. BYRNE: It was done in-house, so to speak.

HAGERTY: Did that always make you feel comfortable? Did you ever wonder if you were getting all the information?

Mr. BYRNE: It did not make me feel uncomfortable. I assumed that they wanted our input or they would not have asked us to do it in the first place.

HAGERTY: Byrne says in the 1990s, the review board heard dozens of cases of alleged abuse. Did they ever recommend that the archdiocese report any of those allegations to the police?

Mr. BYRNE: No, we didn't feel that was part of our responsibility.

HAGERTY: And, Byrne says, not once did the board recommend the archdiocese alert the parishes when a priest was accused of abusing a child, even though that was church policy.

Mr. BYRNE: We assumed that the church was doing what it should do at that time, and what it was required to do.

HAGERTY: One of the cases that went before the board involved a new allegation against Michael Baker. In 1994, Baker had befriended a 14-year-old boy named Luis, who served as an altar boy at St. Columbkille parish. He claimed the sexual molestation began immediately and two years later the boy was spotted outside Baker's room by another priest.

The church notified neither the police nor the parish. None of the church officials involved would comment for the story. But Archdiocesan spokesman Tod Tamberg says they weren't legally obligated to call the police. They did conduct an investigation. Both the archdiocese and the review board concluded that no abuse occurred. And how did they know that?

Mr. TAMBERG: Baker was asked about it. He explained it away, and our mistake at the time was accepting his explanation at face value.

HAGERTY: For four years, the church heard no further complaints about Baker. Then in 2000, two brothers walked into the office of attorney Lynne Cadigan. They were the two boys from Tucson. They detailed their 15-year relationship with Baker. They described the sex and showed her his love letters. Cadigan quickly sent a 14-page letter to Father Baker, and four days later, he called her up.

Ms. CADIGAN: It was shocking. I'd never had a priest confess to me.

HAGERTY: Cadigan says Baker spoke of the many children he had had sex with, in the U.S., Mexico, Thailand and Nepal. He said Cardinal Mahony knew about the abuse, but not the extent. She wrote the archdiocese threatening to sue. Within two months she had a check for $1.3 million. One condition: the settlement would be secret.

Ms. CADIGAN: It was obvious they wanted to sweep everything under the rug immediately. I had never seen such a quick action to cover up and conceal sex abuse.

HAGERTY: After the settlement, Richard Loomis, the vicar for clergy, felt something had to be done about Michael Baker. Here's Loomis in a 2009 deposition obtained by NPR. Here he's talking with Luis's attorney, John Manly.

Mr. RICHARD LOOMIS (Vicar): I made a suggestion that the police should be called.

Mr. JOHN MANLY (Attorney): Did they do that?

Mr. LOOMIS: No.

Mr. MANLY: Who'd you suggest that to?

Mr. LOOMIS: To the cardinal.

HAGERTY: Then Loomis asked if he should alert all the parishes in case there were other victims? Again, the cardinal declined.

Mr. LOOMIS: I was upset because I felt that we should have made the announcements.

Mr. MANLY: Why?

Mr. LOOMIS: Because it was the right thing to do.

HAGERTY: In the deposition, Loomis said he considered resigning. As he waited for the next question, something unexpected happened.

Mr. MANLY: Wait, wait, wait, what are you, what are you doing?

Mr. DONALD WOODS (Attorney): You're trying to set him up.

HAGERTY: The lawyer for the archdiocese suddenly grabs Loomis in an angry bear hug, physically restraining him from talking.

Mr. MANLY: What are you doing?

Mr. WOODS: I'm instructing my client.

Mr. MANLY: I'm in a line of questioning. You just stood up, put your arm around the witness, which he clearly on the video didn't want you to do, and you're trying to get him to be quite because you don't like his answers.

HAGERTY: Shortly after the deposition, Loomis got a new attorney. He was no longer represented by the archdiocese.

In 2002, the Catholic Church sex abuse scandal broke across the country. And in Los Angeles, the archdiocese seemed intent on keeping quiet about the extent of its problem. But soon its secrets were revealed.

(Soundbite of radio show)

Mr. JOHN KOBYLT (Host, The John and Ken Show): KFIA 640, more stimulating talk radio: the John and Ken Show. We're in front of the Los Angeles Archdiocese headquarters...

HAGERTY: Someone in the archdiocese leaked recent emails between Mahony and its attorneys to a popular Los Angeles radio program. The hosts, John Kobylt and Ken Chiampou, set up a studio on the street outside the archdiocese and started reading e-mails.

Mr. KEN CHIAMPOU: Here's a communication from March 27, not very long ago, and it is from Cardinal Mahony: As the drumbeats continue from every side to release the names...

Mr. KOBYLT: In quotes.

Mr. CHIAMPOU: ...I must still point to what I consider our greatest tactical mistake...

HAGERTY: The email goes on to describe Mahony's concern that the church hadn't turned in three of the eight most abusive priests, one of whom was Michael Baker. If the district attorney finds this out, he worries, quote, "I can guarantee you that I will get hauled into a grand jury proceeding and I will be forced to give all the names."

The 68 e-mails read as if the cardinal and his lawyers were more concerned about public relations than the victims. But archdiocesan spokesman Tod Tamberg says you have to read the emails in context.

Mr. TAMBERG: There were legal concerns for the victims. There were legal concerns for those accused. There was blood in the water, in terms of interest by the press. And I think what you see is an archdiocesan leadership faced with a crisis that was still growing and that they were still trying to understand.

HAGERTY: Since then, everything has changed, Tamberg says. Today, if a priest is suspected of abuse, the church pulls him out of active ministry and calls the police. And now the archdiocese employs four retired FBI agents to do the investigations.

Judge Richard Byrne, who still serves on the review board, says Mahony has been a pioneer.

Mr. BYRNE: I think he has been in the cutting edge. The approach that he has taken in Los Angeles can be a model to the rest of the country.

HAGERTY: Byrne says Cardinal Mahony has been wrongly tarnished, and Mahony himself has said he was misled by Michael Baker and other priests.

Attorney John Manly doesn't buy it.

Mr. MANLY: Was he misled when he decided not to notify parishes in 2000? And was he misled when he decided in 2000 to force a confidentiality agreement on the two boys that did come forward? And was he misled in 2000 when he decided not to call the police? He wasn't misled. It was malicious. It was intentional and it was hardhearted.

HAGERTY: Earlier this year, the archdiocese settled the suit with Manly's client, Luis, for $2.2 million. The archdiocese says that 23 people have accused Father Michael Baker of molesting them.

Baker is now serving a 10-year sentence for sexually abusing three boys, and a federal grand jury is investigating whether the Archdiocese of Los Angeles committed fraud by allegedly covering up sexual abuse.

Barbara Bradley Hagerty, NPR News.

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