The judge presiding over the Catholic Archdiocese of Philadelphia priest sex-abuse trial acquitted the cleric in charge of reviewing allegations of sexual abuse or other misconduct by priests with minors of conspiring to endanger the welfare of a 30-year-old man who says a priest attempted to rape him.

Philadelphia Court of Common Pleas Judge M. Teresa Sarmina granted the motion for judgment of acquittal sought by Monsignor William J. Lynn and his co-defendant, the Rev. James J. Brennan, finding that prosecutors did not prove they conspired together to endanger the welfare of M.B. The Legal is not naming the alleged victims.

Sarmina denied the other defense motions for judgments of acquittal.

After the prosecution rested Thursday, the counsel for Lynn will still be defending their client on the charges that Lynn endangered the welfare of the youth allegedly abused by Brennan and endangered the welfare of a separate youth that defrocked priest Edward V. Avery already pled guilty to sexually abusing. Lynn also is still facing charges that he conspired to endanger the welfare of children with Avery.

The lawyer for Brennan still must defend his client against charges that Brennan attempted to rape M.B. and that he endangered the welfare of M.B.

Sarmina did not enumerate reasons for her rulings, except to say that she was denying the defense motion that jurors should not decide whether Lynn endangered the welfare of children as “there also is accomplice liability, not just conspiratorial liability” for the jury to consider.

Lynn was the late Cardinal Anthony J. Bevilacqua’s delegate for investigating priests accused of sexual abuse from 1992 to 2004 when he was the personnel director for priests and serving as the secretary for clergy.

Jeffrey M. Lindy, Lynn’s counsel with Lindy & Tauber, argued that the prosecution had not shown that “Lynn, in doing his job, engaged in conduct that nearly certainly” endangered children.

Lindy also argued against the conspiracy charges.

“For a conspiracy to be made out there has to be evidence that Monsignor Lynn, along with church leaders, worked to hurt kids,” Lindy said.

William J. Brennan, the attorney for defendant James Brennan, said that unlike so many other priests about whom prosecutors produced evidence there were no “ticking time bombs.”

There was no secret-archive file on James Brennan like the files the archdiocese kept on Avery and other priests who had been accused of serious problems such as sexual abuse, attorney Brennan argued.

The other evidence prosecutors pointed to was that his client had loud parties with adults when he lived in a religious institution; that a former Catholic-school student of unknown relation was known to have lived with Brennan at the institution; and that Brennan had been seen to wrestle with M.B., attorney Brennan said.

An eyewitness to the wrestling said he did not view it as sexual, the student was above the age of majority, and the parties were attended by adults, attorney Brennan said.

“Unlike any other file in this case there is nothing to indicate Father Brennan is a problem priest and Monsignor Lynn should have done something about it,” attorney Brennan said.

Prosecutor Patrick Blessington argued that, with Lynn’s past knowledge of the grooming that sexual predators conduct of youths and that sexually abusive priests would often live for periods of time with the youths they abused, that it should have struck alarm bells that James Brennan was living with a young man.

“‘Based upon everything I know, based upon a duty of care I have taken on in assigning priests,’” Lynn should have said to himself, Blessington argued, those were warning signs that should have caused Lynn to investigate Brennan.

There also was a warning sign that Brennan told Lynn he needed to go on a leave of absence to deal with a course of sexual and other abuse he suffered as a child, Blessington said, because it is commonly known that many of the abused turn out to be abusers.

It was during Brennan’s leave of absence that he allegedly abused M.B.

In the last prosecution evidence to go the jury, a time line showed that Lynn listed Avery as guilty of sexual misconduct with a minor after culling a list of 35 priests alleged or admitted to have sexually abused minors in 1994. But it was not until June 2003 that a preliminary investigation was opened into Avery and December 2003 that Avery was excluded from ministry.

Avery has admitted sexually abusing D.G.

At the apex of the prosecution’s case, the jury was allowed to see for themselves the gray folder that contained the list Lynn generated in 1994 of the 35 priests alleged or admitted to have sexually abused minors out of a totality of 323 secret-archive files.

Bevilacqua later ordered in 1994 that the copies of the list be shredded, according to a memorandum entered into evidence in the case.

But iterations of the list were saved in the safe kept in a file room for the Office of the Secretary for Clergy.

The safe was drilled open in 2006 and the file folder removed, but the list and other documents were not turned over to prosecutors in response to discovery subpoenas until early this year.

Lynn testified to a Philadelphia investigating grand jury in February 2004 that, when he was still the secretary for clergy, he looked for the list he and a subordinate curated of the 35 priests but he was not able to find it, according to a time line moved into evidence Thursday.

Lynn also testified that he did not ask Bevilacqua and two other superiors if they had copies of the list.

During Thomas A. Bergstrom of Buchanan Ingersoll & Rooney’s cross-examination of Detective Joseph Walsh of the Philadelphia District Attorney Office’s special investigations unit, Bergstrom emphasized that the Rev. James E. Molloy of the Office for Vicar of Administration said in handwritten notes that he destroyed the copies of the list, including the original received from the secretary for clergy.

Walsh said Molloy was shredding his original, while Bergstrom said, “That’s what you want to think it says.”

Molloy died in 2006, Walsh said.

Amaris Elliott-Engel can be contacted at 215-557-2354 or aelliott-engel@alm.com. Follow her on Twitter @AmarisTLI.