Weeks before prosecutors say he tried to rape a 14-year-old boy, the Rev. James J. Brennan called the clergy office at the Archdiocese of Philadelphia.

At the time, Brennan had just started a leave of absence to deal with "inner turmoil" he blamed in part on being sexually abused as a child.

Brennan complained to Msgr. William J. Lynn, who ran the clergy office, that other priests had been gossiping that he really took the leave so he could "shack up" with one of his former students at Cardinal O'Hara High School.

"I told him not to be concerned about the rumors, that we only take facts as we find them," Lynn wrote in a June 1996 memo.

Prosecutors showed Common Pleas Court jurors that confidential document Tuesday as they sought to prove that Lynn ignored signs of an allegedly abusive priest. Lynn had heard the same rumor, and had previous reports that the priest was sharing his apartment with a young man, records show.

Nowhere in the same file, Assistant District Attorney Jacqueline Coelho noted, was evidence that Lynn investigated the rumor or tried to find the student. "None whatsoever," Detective James Dougherty testified.

For seven weeks, Brennan and Lynn have sat a few feet apart at the defense table in the landmark clergy sex abuse trial, though they might as well have been in separate courtrooms. The testimony marked the first time prosecutors introduced evidence linking the clerics, a sign that their case may be nearing an end.

Lynn is accused of endangering children by not removing priests he knew or suspected would abuse minors. Brennan is charged with assaulting the teen.

His records were discussed on the same day a Philadelphia police officer described Lynn's appearing to minimize abuse allegations against a notorious priest in 2001.

The alleged evidence against Brennan is more subtle, and is potentially critical to the case. Prosecutors say he tried to rape the boy one night in 1996 when the teen stayed at his West Chester townhouse.

Brennan's lawyers have disputed the claim, calling the accuser a liar who made up the allegation in a bid for money or to excuse a decade of drug use and petty crime. They will attempt to build on the argument during cross-examination Wednesday.

The confidential records shown to jurors portrayed Brennan, ordained in 1989, as a young priest tortured by something, regularly questioning his vocation and prone to conflicting statements. During a conversation with Cardinal Anthony Bevilacqua, he freely recounted being sexually abused as a child, according to a memo the cardinal wrote, but later denied telling anyone he had been abused, records show.

His longest assignment was from 1991 to 1996, when Brennan taught at Cardinal O'Hara in Springfield, Delaware County, and lived at Divine Providence Village, a nearby church-owned residential treatment center. In 1995, nuns at Divine Providence privately complained to archdiocesan officials that Brennan hosted loud parties and shared his apartment with a young man.

Brennan had told the nuns and others that his boarder was his nephew. Years later, he admitted it was not a relative but one of his former high school students he let live there to save money.

After his leave of absence, Brennan returned to ministry as a parish priest in 1997, first in Philadelphia, then Bucks County. By 2000, months after he proclaimed he was happy at his latest assignment, Brennan again was seeking a transfer, this time to a Trappist abbey in South Carolina.

In a letter to Lynn, he said the monastic life was appealing because some of his deepest reflection came in dark solitude. He shared a journal passage he said he wrote before dawn one day.

"Here, deep within myself is the primordial struggle being lived out in a tormented state of unbridled passion," Brennan wrote. Another passage read: "And so I scrub my face and hands to present a clean man for the world to see, this filth and stench of my wanton failures of yesteryear are washed away."

Prosecutors cited those passages more than once in the months before the trial, suggesting the priest's inner turmoil was sexual. But nowhere in the pages read to jurors did Brennan explain what he meant.

Lynn and Bevilacqua questioned Brennan's true reason for wanting to become a monk but ultimately agreed to the transfer. Less than a year later, he returned to the Archdiocese of Philadelphia, where he stayed an active priest until 2006, when the attempted rape accusation surfaced.

Earlier Tuesday, a Philadelphia sex crimes officer described meeting Lynn in 2001. The officer, Denise Holmes, was investigating a complaint from a woman who said the Rev. Nicholas Cudemo molested her 20 years earlier when she was a student at the school in St. Irenaeus Parish in Southwest Philadelphia.

According to Holmes, Lynn said he knew of no accusations against Cudemo from that time. He said the only claims against Cudemo were reported in 1991 by three of the priest's female relatives. Lynn also claimed not to know where Cudemo was living, except for "Florida, maybe."

Assistant District Attorney Patrick Blessington said that by the time the officer questioned Lynn, the clergy secretary had received a dozen sex-abuse complaints against Cudemo and knew the priest's address in Orlando because Cudemo had been lobbying Lynn to recommend him for a parish assignment in the Orlando Diocese.

Contact John P. Martin at 215-854-4774 or at jmartin@phillynews.com. Follow him @JPMartinInky on Twitter.

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