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Matt Rourke, Associated Press
The Rev. James J. Brennan returns to the Criminal Justice Center in Philadelphia following a break Monday, March 26, 2012. Brennan is charged with the attempted rape of a 14-year-old boy in 1996.

PHILADELPHIA — After nine years and two grand jury reports, prosecutors have brought a landmark case to trial that explores how the Archdiocese of Philadelphia dealt with child sex-abuse complaints against scores of Roman Catholic priests.

Monsignor William Lynn is the first U.S. church official ever charged over his handling of abuse complaints. He supervised more than 800 priests as the secretary for clergy in Philadelphia from 1992 to 2004.

Prosecutors charge that Lynn kept dangerous priests in parish work around children to protect the church's reputation and avoid scandal. They say the church kept secret files dating to 1948 that show a long-standing conspiracy to doubt sex abuse victims and protect priests.

Assistant District Attorney Jacqueline Coelho called the case "a battle between right and wrong within the archdiocese and the office of secretary for clergy."

But defense lawyer Thomas Bergstrom said Monday that Lynn had the "ugly job" of overseeing sex abuse complaints but that Cardinal Anthony Bevilacqua alone determined priest assignments and transfers.

"There is documentary evidence that the sexual abuse of children happened in the Catholic Church," Bergstrom said. "We're not going to run from that. He (Lynn), perhaps alone, is the one who tried to correct it."

Lynn, 61, appeared solemn in court, where he has appeared often the past few months for pretrial hearings and jury selection. He has been under investigation for eight years, through two grand jury investigations that blasted Bevilacqua and his successor, Cardinal Justin Rigali, saying they covered up child sex complaints lodged against more than 60 priests.

But Lynn was the only supervisor charged. If convicted of two counts each of conspiracy and child endangerment, Lynn faces up to 28 years in prison.

Bevilacqua died in January, although the jury might see a videotaped deposition he gave weeks earlier. The trial could last several months.

Besides Lynn, Rev. James Brennan is on trial, accused of raping a 14-year-old boy in 1996. Both men entered not guilty pleas Monday. A third defendant, defrocked priest Edward Avery, pleaded guilty last week to charges in the case.

Defense lawyers have long planned to attack the credibility of the two accusers, who have struggled with drug addiction and have criminal records. But that strategy took something of a hit when Avery entered the surprise guilty plea Thursday.

Avery, who moonlighted as a disc jockey and adopted six Hmong children during his years in the priesthood, admitted that he sexually assaulted a 10-year-old altar boy in a church sacristy in 1999. That victim accused another priest and his sixth-grade teacher of raping him during his parochial school years. They will go on trial separately because neither was an archdiocesan priest reporting to Lynn.

Brennan's accuser has convictions for theft and filing a false police report and called none other than the person he accused of abusing him when he needed to do court-ordered community service, a defense lawyer said.

"If you don't believe (him) ... the case is over," said lawyer William Brennan, who is not related to his client.

Avery's plea also acknowledged that the archdiocese kept him in ministry despite being aware of an earlier complaint. That complaint, dating to 1992, was detailed in court Monday by the first witness to take the stand in the trial.

A Philadelphia detective read a 1992 letter from a medical student that said Avery had once gotten him drunk and molested him after a DJ stint at a West Philadelphia nightclub and later on a ski trip.

"I do not want money or any kind of media scandal," the accuser wrote. "I need to know that he has been evaluated and treated for this disorder and his threat to other impressionable young men is gone."

The archdiocese interviewed Avery, who denied the allegations before saying they could have happened when he was drunk.

"I thought he was a potential (priest). I was so good to him," Avery told Lynn and Bishop Joseph Cistone in a 1992 interview, according to an archdiocesan memo read in court.

Avery was sent for inpatient therapy for eight months before returning to the ministry. He sexually assaulted the altar boy seven years later, he admitted Thursday.