The charges against Msgr. William J. Lynn are narrow: that the former Archdiocese of Philadelphia official endangered children by letting two priests live or work in parishes despite signs they might abuse minors.

But the case prosecutors finished presenting Thursday stretched beyond those confines. Day after day in Courtroom 304 of the city's Criminal Justice Center, the church itself seemed to be on trial.

Over eight weeks, jurors saw a parade of witnesses and close to 2,000 documents, some decades old, that detailed what bishops, pastors priests, and church officials knew and did about Philadelphia-area priests suspected of abusing children.

Together, the evidence pointed to a long-standing culture in the hierarchy - and at times the ranks below - that chose secrecy over transparency and the welfare of the institution over victims.

"It was all about the good of Mother Church," Assistant District Attorney Patrick Blessington said in arguments to the judge Thursday. "They cared about money, they cared about the business of the church, not the flock and not the parishioners."

Lynn, a former secretary for clergy and the first church official nationwide to be tried for covering up child sex abuse, may yet be vindicated. His lawyers, Thomas Bergstrom and Jeffrey Lindy, scored one victory when Judge M. Teresa Sarmina dismissed as unproved charges that Lynn conspired with his codefendant, the Rev. James J. Brennan.

Sarmina left intact the more serious allegations: that Brennan tried to rape a 14-year-old boy in 1996 and that Lynn's failure to remove Brennan and another priest, Edward Avery, constituted child endangerment.

Lynn's defense team opens its case Tuesday, hoping to build on its contention that he is a scapegoat, a middle manager being unfairly held accountable for the sins of superiors.

They say that Lynn had perhaps the ugliest job in the archdiocese - policing wayward colleagues - and that he, more than anyone else in the church hierarchy, strove to keep dangerous priests away from children.

But there are no lawyers at the trial to defend the archdiocese, its former and current leaders, or the scores of accused priests and others whose names have surfaced, often in unflattering ways.

"It's kind of a spreading stain that you see in this trial," said Terence McKiernan, president of, which catalogues clergy sex-abuse cases worldwide. "It's becoming clearer and clearer that as reprehensible as the people of the top were . . . it really does extend down to the ranks of pastors and other priests."

The bulk of the evidence had been aired before, in a 2005 grand jury report that ran nearly 500 pages. It ended without charges because the allegations were too old to be prosecuted. Church leaders dismissed the report as biased and urged Catholics to ignore it.

If that report was a script, the trial has been its curtain-raising debut, performed in 32 daylong acts. The cast included many middle-aged men, former altar boys who tearfully recounted decades-old incidents as if they had happened last week.

The images they painted were searing: a 13-year-old son of a Philadelphia police officer, clutching a penknife in terror and hiding in a cabin after being fondled all night on a camping trip with the Rev. Francis Trauger; another boy, waking up naked next to the Rev. Thomas Smith in a motel room after the priest stuffed ice cubes in his underwear and got him so drunk he passed out; a Bucks County teen forced to engage in oral sex with the Rev. David Sicoli after they drove to Veterans Stadium to buy Phillies playoff tickets in the early 1980s.

That boy had been identified by church officials as a potential victim in 1983, the church's secret files showed. Two decades passed before anyone called to ask him about Sicoli.

"Ever since the scandal in Boston, I kept waiting - when is it going to happen? When is this guy going to get his?" the man told jurors.

Like nearly all the priests mentioned at trial, Sicoli was defrocked but never charged.

Prosecutors were allowed to introduce such evidence to suggest that Lynn was deeply aware of the problem of clergy sex abuse and that his decisions followed a pattern of transferring priests and burying abuse complaints.

Jurors also heard hours of Lynn's own statements to the grand jury a decade ago. Back then, he acknowledged that he recommended removing priests from ministry only if they admitted abusing a minor or had been found to be attracted to children or adolescents. He was not trained to investigate, he said. Even when he learned the names of potential victims, he did not try to find or contact them, Lynn said, for fear of "re-victimizing" them.

Those he did meet were not always satisfied.

"My feeling was that they didn't really care - they were just going through the motions," said one witness, a woman who met Lynn in 2002 to discuss her complaint that the Rev. Edward DePaoli had fondled her when she was in grade school. She also got an audience with Cardinal Anthony J. Bevilacqua, the woman said. He gave her a rosary and a prayer book.

Another accuser, a Catholic nun who reported in 1991 that she and other relatives had been abused as teens by their cousin, the Rev. Nicholas Cudemo, coolly admonished Lynn from the witness stand. He may have lacked the authority to remove abusive priests, she said, but he should have done more. "You can also say, 'I cannot do this,' " she said, looking toward Lynn.

The clergy secretary was not the only one with that opportunity. Many records shown to jurors were drafted, signed, or witnessed by other clerics and officials, sometimes years or even decades before he took the job investigating complaints.

Lynn's predecessor in the clergy office, Msgr. John J. Jagodzinski, left the Rev. Peter Dunne in parishes after doctors diagnosed Dunne as a pedophile and described him as "a sick man" and "a powder keg" poised to explode, the records showed.

Lynn had three assistants over 12 years - the Rev. James D. Beisel, the Rev. Michael McCulken, and the Rev. Vincent Welsh - who routinely accompanied him during interviews or drafted his memos about abuse complaints. (Each is likely to be called as a defense witness this week.)

The graphically detailed memos were often shared with Bevilacqua, Bishop Edward Cullen, or Joseph Cistone, assistant vicar for administration.

The evidence also entangled Lynn's successors, including Bishop Timothy Senior, who took over the clergy office in 2004.

On Monday, Senior and the archdiocese's top in-house lawyer, Timothy Coyne, took the stand in succession, each pleading fuzzy memories or pointing fingers over who knew what about a gray folder that was missing for at least a decade.

The folder, turned over to prosecutors this year, held a 1994 list drafted by Lynn identifying three dozen priests who had admitted or were suspected of sexual misconduct with minors. Coyne and Senior both denied realizing the list was in the folder or giving the order to stash it in a file drawer.

"With all due respect, Bishop, it sounds like you're blaming him and he's blaming you," Blessington told Senior.

Other witnesses offered more subtle testimony about how people often missed - or ignored - signs of abuse.

Shirley Birmingham, a parishioner at St. Gabriel Church in Stowe, Montgomery County, in the mid-1990s, testified that she was alarmed to learn that DePaoli had an unmarked video in brown wrapping paper delivered to the parish rectory despite having been convicted of possessing child pornography. But when Birmingham brought the package to the Rev. John Marine, the vicar for the county, "the most interest he seemed to have was the fact that [DePaoli] did the homily each week," she told jurors.

The Rev. Joseph Okonski said he was stunned to find sadomasochistic pornography and a sexually graphic love letter to a boy in the Rev. Michael Murtha's bedroom in 1995. But when Okonski reported his find to the Rev. James Shield, their pastor at St. Anselm's in Philadelphia, Shield "did nothing," he said.

Priests who pushed back often did so at their own peril. The Rev. Michael Picard, the pastor of St. Andrew Church in Newtown, testified that he objected when Lynn tried to send him an assistant pastor, the Rev. Donald Mills, whose illicit relationships with men were no secret.

"I told him that there was a serious problem that needed to be looked into," Picard testified, "and that we needed to resolve problems instead of transferring problem priests around."

Instead, Picard's parish was left short-staffed, he was investigated by a priest personnel board for disobeying an order, and he waited more than a decade to be elevated to monsignor.

The Rev. Michael Hennelly was one of the priests who complained about Sicoli's unhealthy relationships with boys at Our Lady of Hope in Philadelphia in 1993. When the complaints went unheeded, Hennelly requested a transfer.

"I had to make a personal decision," he told jurors. "For my well-being, I couldn't live and work there."

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Staff writer Joseph A. Slobodzian contributed to this aticle.

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