For weeks the words of Msgr. William J. Lynn in testimony before a 2004 Philadelphia grand jury investigating clergy sexual abuse were used against him by state prosecutors.

They intensified their use of the testimony and a trove of hundreds of archdiocesan memos and letters, narrated by Philadelphia police detectives and assistant district attorneys along with some four dozen witnesses, to show jurors in a landmark criminal case that Msgr. Lynn, 61, and former secretary for clergy of the Archdiocese of Philadelphia, was part of a conspiracy to protect priests and endanger children.

In a significant decision the day the prosecution rested its case, on May 17 presiding Judge Teresa Sarmina dismissed two counts of conspiracy against Msgr. Lynn and another defendant, Father James J. Brennan, 48.

Only two counts of endangering a child remain against Msgr. Lynn: one related to former priest Edward V. Avery, who pleaded guilty to sexually assaulting a boy in 1999; and another charge related to Father Brennan.

The latter now faces one charge of attempted rape, downgraded from the charge of rape in the Philadelphia grand jury presentment of 2011. His only accuser has testified that as a 14 year old, he and the priest slept clothed in the same bed in 1996.

Both Msgr. Lynn and Father Brennan have pleaded not guilty to their charges.

At the conclusion of the eighth week of the trial at the Criminal Justice Center in Philadelphia, the state’s case built to a crescendo.

The Archdiocese’s top lawyer, Timothy R. Coyne, currently on leave of absence, voiced frustration with top administrators of the Church concerning a list of 35 priests suspecting of child sexual abuse which was compiled by Msgr. Lynn in 1994.

“Somebody lied to me,” he said on the witness stand as prosecutors and Msgr. Lynn’s defense lawyers sought to use the same piece of evidence to their own advantage.

His defense team has contended that the priest compiled the list to identify and resolve the problem of clergy sexual abuse in the Archdiocese. The prosecution has painted the list as evidence of a conspiracy to conceal the nature and scope of the same problem.

Coyne testified that when he asked archdiocesan leaders about the list in 2002 no one knew of its whereabouts. A memorandum produced at trial indicated the list was ordered to be shredded by Cardinal Anthony Bevilacqua, Archbishop of Philadelphia in 1994. But a copy of it was kept secretly by a top administrator, Msgr. James Molloy, in his personal safe at the Archdiocesan Pastoral Center.

It was only opened in 2006, and the document discovered, after the priest’s death in 2006.

The list was turned over to the court in February of this year just weeks before the landmark trial began.

Msgr. Lynn’s defense has tried to show jurors that Msgr. Lynn’s superiors, including Cardinal Bevilacqua, Msgr. Molloy, then-Msgr. Edward Cullen and then-Father Joseph Cistone, were responsible for assigning priests with allegations of sexual misconduct or abuse, with the Cardinal possessing ultimate authority for assignments and policies to deal with the priests.

The Cardinal led the Philadelphia Archdiocese from 1988 to 2003 and died last January. Msgr. Molloy died in 2006. Bishop Edward Cullen is the retired bishop of Allentown and Bishop Cistone is the current bishop of Saginaw, Mich.; neither bishop has been called to testify in the case.

Prosecutors in the case allege that Msgr. Lynn, the highest ranking priest in the United States to be charged with crimes related to the clergy sexual abuse scandal, endangered children by recommending assignments where Avery and Father Brennan had access to children.

Msgr. Lynn’s lawyers begin their defense case starting the week of May 21.