"On-the-job training" was how Msgr. William J. Lynn described his preparation to become the Archdiocese of Philadelphia's chief investigator of priests accused of sexually abusing minors.

That's what Lynn told a Philadelphia grand jury in 2004 and that portrait - of an innocent, inexperienced priest thrust into a job that required the training of a lawyer, detective and psychologist - has been a mainstay of his defense in the landmark Common Pleas Court trial in which he is accused of enabling pedophile priests to continue to prey on children.

On Wednesday, a Philadelphia prosecutor worked to undercut that image, using archdiocesan documents to portray Lynn as a church official fully engaged in a campaign initiated by the late Cardinal Anthony J. Bevilacqua to control damage to the church's reputation and defend it from victim lawsuits.

"Recon" reads Lynn's handwritten note on a November 1993 copy of a Philadelphia magazine article profiling Stephen Rubino, a New Jersey lawyer then trying to use racketeering laws to sue the church over its handling of pedophile priests. Lynn's handwritten notes then outline a legal and public-relations campaign to counter Rubino and his allegations.

"Tenacious," "not a lawyer's lawyer," and "tries cases in the press" were some of Lynn's notations on a legal pad projected on a screen by Assistant District Attorney Patrick Blessington as the prosecution began winding down its case against Lynn, 61.

Prosecutors are expected to conclude their case Thursday following cross-examination of Detective Joseph Walsh, of the District Attorney's Office, whom Blessington uses to narrate and describe church documents discovered during the investigation.

The documents contain virtually no mention of the priests' alleged victims. Rather, they outline a broad effort to categorize the accused priests, justify the church's actions, and protect the archdiocesan hierarchy from the burgeoning scandal.

A 2002 memo from Bishop Joseph Cistone to Lynn, for example, refers to the Pennsylvania Catholic Conference, the church's lobbying arm in Harrisburg, and its efforts to prevent the legislature from extending the deadline for purported victims of sexual abuse to sue the church.

A 1994 memo calls to Lynn's attention the special committee created by Bevilacqua and other Pennsylvania prelates to devise ways to safeguard church Secret Archives documents from being subpoenaed for use in victims' civil lawsuits.

The documents were among a cache - including a changing list of pedophile priests compiled by Lynn and his assistant, the Rev. James D. Beisel, in 1994 - that archdiocesan lawyers say were shredded on Bevilacqua's orders. Lynn described the list and documents to the grand jury eight years ago but testified that he could not find them.

The documents contradict Lynn's claim in his grand jury testimony that he voluntarily began a review of the Secret Archive after he became secretary for clergy in 1992. Instead, memos show Bevilacqua ordering Lynn and Beisel to conduct the review as part of the Archdiocese's preparation of a defense against a feared wave of lawsuits.

One January 1994 memo by Beisel, attached to a 14-page list of 323 priests accused of a variety of misconduct, including sexual abuse, includes a yellow sticky note reading: "Father Lynn's copies."

Earlier trial testimony revealed that the documents were found in 2006 locked in a safe at archdiocesan offices in Center City but, inexplicably, not turned over to the District Attorney's Office until February.

Blessington has argued that the documents showed that Lynn and others lied to the grand jury in an attempt to downplay allegations that pedophile priests were regularly transferred from parish to parish, enabling them to victimize other children.

Lawyers for Lynn have denied the allegations, and Lynn has pleaded not guilty to charges of conspiracy and endangering the welfare of children.

In addition to documenting Lynn's activities during his 12 years as secretary for clergy, the documents include intriguing hints of other aspects of the church's handling of wayward priests:

A March 11, 1994, memo by Lynn to an official of a Michigan treatment center for priests with sexual and other problems that seems to show an attempt to distance Bevilacqua from the problem: "I request that all reports to the Archdiocese of Philadelphia be forwarded directly to me. Cardinal Bevilacqua prefers that he not be copied materials."

A Dec. 7, 1987, memo from the Rev. John W. Graf, an assistant in the office that preceded the Office for Clergy, to then-Cardinal John Krol that discusses a list of archdiocesan priests who have been accused of misconduct.

Two 1994 handwritten lists by Lynn and Beisel that mentioned the names of seven "extern priests" - priests ordained in other dioceses but working in the Philadelphia archdiocese - against whom allegations of sexual abuse of minors had been established. None of those names had been mentioned in previously released church documents.

Contact Joseph A. Slobodzian at 215-854-2985, jslobodzian@phillynews.com, or follow him on Twitter @JoeS

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