NEW YORK — In the aftermath of Archbishop Carlo Maria Viganò’s sensational claim that Pope Francis knew about misconduct allegations against ex-Cardinal Theodore McCarrick in 2013 and ignored them, Viganò’s own handling of a sex abuse crisis in the U.S. has come under fresh examination.

In June 2015, Archbishop John Nienstedt of Saint Paul-Minneapolis resigned his post following a turbulent in-house archdiocesan investigation into claims of sexual misconduct, just ten days after prosecutors brought charges against the archdiocese for its “failure to protect children.”

Court documents from a settlement between the archdiocese and Ramsey County prosecutors reveal a tug-of-war between auxiliary bishops and priests within the archdiocese, along with other internal and external whistleblowers, as well as the now-retired nuncio.

In recent days, Viganò has rejected claims that he tried to interfere in the investigation. Yet new interviews with some of the pivotal players — along with confirmations that two U.S. cardinals were involved to varying degrees with discussions over Nienstedt’s potential removal — suggest that question marks about his role have not yet been resolved.

The Launch of the Investigation

In January 2014, Nienstedt agreed to an internal investigation into claims from two priests within the archdiocese who had accused him of “unwanted touch.”

Father Dan Griffith, who served as the archdiocese’s Safe Environment coordinator and later as the liaison between the archdiocese and the outside legal counsel tasked with leading the investigation, Greene Espel, penned a 2014 memo saying the archdiocese was in possession of letters from a gay bar and strip club called the “Happy Tap,” in Ontario, Canada, claiming that Nienstedt was a regular presence there.

In addition, according to affidavits signed during the investigation, Nienstedt was also a close personal friend of Father Curtis Wehmeyer, who, in 2013, was convicted for sexually abusing two boys at his church.

Court documents reveal that Nienstedt was responsible for advancing the career of Wehmeyer, going against counsel of others within the archdiocese who had warned him of a history of predatory behavior and heavy drinking.

In March 2015, Francis issued a decree removing Wehmeyer from the priesthood, just one month prior to Nienstedt’s resignation.

Nienstedt’s dismissal of the warnings he received on Wehmeyer, along with his broader handling of the archdiocese’s sexual abuse policies, led to the resignation of his former chancellor for canonical affairs.

Jennifer Haselberger told Crux she decided to leave because “we needed to radically alter the Catholic Church’s approach to sexual misconduct and sexual abuse. I believed in the commitments made in the 2002 Charter and was frustrated to discover them to be empty promises.”

[The reference is to a 2002 charter adopted by the U.S. bishops in Dallas pledging the Church to combat child sexual abuse aggressively.]

“I was further troubled by the lack of urgency that was exhibited, especially when presented with cases of abuse perpetrated more than a decade after the crisis that was supposed to have resulted in a zero tolerance policy,” she said.

Haselberger was the first employee within the archdiocese to go public with her concerns, leading her to pen a 107-page affidavit describing the “cavalier attitude toward the safety of other people’s children” of archdiocesan officials.

Moreover, in addition to new information uncovered in the in-house investigation, according to the Griffith memo, Nienstedt’s predecessor Archbishop Harry Flynn had conveyed concerns about Nienstedt’s sexual behavior to Italian Cardinal Giovanni Battista Re while he was prefect for the Congregation for Bishops in Rome.

(Re is among the individuals named in Viganò’s 11-page statement released on Sunday, the heart of which is his charge about Pope Francis, for reportedly opposing McCarrick’s appointment to lead the Archdiocese of Washington.)

Destroying evidence?

The mounting evidence against Nienstedt from the Greene Espel investigation led auxiliary bishops Lee Piché, who was overseeing the investigation, and Andrew Cozzens to travel to Washington, D.C., in April 2014 to meet with the nuncio regarding the investigation in hopes “to reach a pastoral resolution for the good of the archdiocese.”

Nienstedt — who during the years of 1980-1985 worked at the English desk of the Vatican’s Secretary of State as a colleague of Viganò — joined the trip to Washington, which included a meeting between Piché, Cozzens, and Viganò, and then a separate private meeting between Nienstedt and Viganò.

In his memo, Griffith says he believes Nienstedt used that meeting to convince the nuncio that the allegations against him were false. Viganò is reported to have followed up the Washington meetings with a call to Piché, encouraging him to “wrap up” the investigation.

Griffith goes on to note in his memo that the nuncio ordered the auxiliaries to end the investigation and no longer pursue further leads — despite the fact some 24 new leads remained to be interviewed by the outside counsel.

In turn, Piché and Cozzens responded to Viganò with a letter expressing their disagreement with the directive to shut down the investigation and noting that it would be seen as a cover-up.

According to the Griffith memo, Viganò responded to that letter with a request that it be destroyed.

“The destruction of evidence is a crime under federal law and state law, and the fact that this request was made of you by a papal representative to the United States is most distressing,” wrote Griffith to Piché.

Viganò’s Denials

In a statement earlier this week, Viganò said claims that he tried to close the investigation are “false.”

“Father Griffith was not present during my meeting at the Nunciature with the Archbishop and the two Auxiliaries on April 12, 2014, during which several affidavits containing accusations against Archbishop Nienstedt were handed to me,” the archbishop said in statement given to LifeSite, a conservative Canada-based Catholic website.

The former nuncio said one of the affidavits collected by the firm included an accusation Nienstedt had had an affair with a Swiss Guard during his service in the Vatican 20 years earlier.

Nienstedt, however, has denied all allegations of sexual impropriety, saying he is heterosexual and has always been faithful to his promise of chastity.

“Private investigators from the Greene Espel firm had conducted an inquiry in an unbalanced and prosecutorial style, and now wanted immediately to extend their investigation to the Pontifical Swiss Guard, without first hearing Archbishop Nienstedt,” Viganò said.

“I suggested to the bishops who came to the Nunciature on April 12, 2014, that they tell the Greene Espel lawyers that it appeared to me appropriate that Archbishop Nienstedt be heard before taking this step – audiatur et altera pars – which they had not yet done. The bishops accepted my suggestion,” he continued.

Viganò said he received a letter signed by the two auxiliary bishops asserting he suggested the investigation should be stopped, and he asked Piché to remove that accusation from the archdiocesan computer system and archives.

“I insisted on this not only to protect my name, but also that of the Nunciature and the Holy Father, who would be unnecessarily harmed by having a false statement used against the Church,” the archbishop said.

Viganò also claimed Jeffrey Lena – an American lawyer working for the Holy See – went to the Congregation for Bishops and found documents “proving that my conduct had been absolutely correct.”

The former nuncio also furnished LifeSite with two letters backing his claim. Lena declined a Crux request for comment.

The first letter furnished to LifeSite was by Viganò, dated Nov. 13, 2014, and addressed to Cardinal Marc Ouellet, the head of the Vatican’s powerful Congregation for Bishops, in which the archbishop denies he told the bishops that the Vatican would not allow an investigation into the allegations against Nienstedt.

The second was by Piché, dated Nov. 20, 2014, and also addressed to Ouellet.

In the letter Piché said he was clarifying Viganò’s comments during the April 12 meeting, “correct[ing] my interpretation of his instructions.”

In an effort to seek support to press the investigation, Cozzens sought the counsel of Cardinal Timothy Dolan of New York. Cozzens was reportedly advised by Dolan to “write everything down,” though Dolan, through a spokesman, said he couldn’t recall using those exact words.

Joseph Zwilling, Dolan’s spokesperson, told Crux that Cozzens did consult Dolan about the Neinstedt investigation, showing what Zwilling said Dolan described as a “sincere desire to get to the truth.”

Zwilling also said Dolan encouraged Cozzens to bring the information directly to Viganò in his role as the pope’s ambassador and to “be candid.”

In addition to Dolan, Crux has learned that Cardinal Sean O’Malley, who heads the Pontifical Commission for the Protection of Minors, intervened in the matter, including directly petitioning Francis to accept Neinstedt’s resignation.

Terrence Donilon, a spokesman for O’Malley, confirmed to Crux that the Boston cardinal spoke personally to Francis and other Vatican officials to support the resignations of both Neinstedt and Bishop Robert Finn of Kansas City, who was convicted in 2012 of a misdemeanor charge of failure to report a priest on suspicion of child abuse and sentenced to probation.

Giving in to the “Enemies of the Church”

In addition to O’Malley’s intervention in Rome, Crux has learned that Viganò was warned about the archbishop of the Twin Cities on at least one other occasion — this time by a prominent U.S. Catholic leader who asked not to be named, and who says he tried to persuade Viganò to take action.

He told Crux that the former papal envoy vociferously rejected his pleas, saying it would be a mistake to “give in to the enemies of the Church, the media, and the lawyers attacking the Church.”

On June 15, 2015, the Vatican announced that it had accepted the resignations of Nienstedt, along with Piché, under the terms of canon law that allow for a bishop to step aside for a “grave reason” that means he can no longer fully exercise his office.

Following his resignation, Nienstedt found an institutional home as a consultant to the Napa Institute, a California-based organization founded by Tim Busch, a prominent Catholic conservative, whose annual summer conference brings together several hundred wealthy Catholic philanthropists and high-ranking Catholic prelates at his Napa Valley resort.

From 2016 until earlier this month, Nienstedt was a regular presence at the Institute’s conferences and served as a regular chaplain at their pilgrimages throughout Europe.

On August 15, the Institute announced that the former archbishop was no longer affiliated with their programs.

“In light of the Napa Institute’s efforts to promote a faithful lay-led reform, Archbishop Nienstedt has stepped aside from his responsibilities with the Napa Institute effective immediately,” read the statement.

Meanwhile, Busch has told the New York Times that he was aware of Viganò’s letter two weeks prior to its release — which according to his expressed timeline would have been just days before his Institute announced Nienstedt’s departure.

Busch — who, was also a co-honoree with Viganò at the Rector’s Dinner of the North American College, the national seminary of the U.S. hierarchy, in 2016 — has publicly praised Viganò for the great service he provided the Church in the release of his letter.

Following Viganò’s letter, some of the most prominent Catholics to express support for the former nuncio are also a part of the Napa Institute’s leadership.

Archbishop Charles Chaput of Philadelphia, Archbishop Salvatore Cordileone of San Francisco, Bishop Robert Morlino of Madison, Wisconsin, and Bishop Steven Lopes of the Personal Ordinariate of the Chair of Saint Peter for former Anglicans, are all ecclesial advisors to the Napa Institute and are among the dozen U.S. bishops who have weighed in on the Viganò testimonial.

In addition, on Thursday, Napa Institute board member Mary Rice Hasson of the Ethics and Public Policy Center was one of the leading individuals to launch an online petition for women demanding that Francis respond to Viganò’s allegations.

Busch declined a Crux request for comment.

Hasson, however, told Crux that she did not not draft the letter in her capacity as a board member of the Napa Institute nor did she discuss the matter with Busch or have prior knowledge of Viganò’s forthcoming letter.

“This is an action from the hearts of women, springing from a sincere desire to help the Pope realize that we need his leadership and his answers, because we want to trust the Church going forward.  To portray the Letter as anything other than that is untrue and unfair,” she maintained.

While the Vatican continues to stand firm in its resolve not to comment, and reaction in the United States to the Viganò accusation breaking primarily along ideological lines, in the attempt to better understand Viganò’s potential motivations and his credibility, many believe his handling of the Nienstedt affair serves as a Rorschach test.

Writing in 2014, Griffith said of the situation, “What has unfolded in the face of compelling evidence amounts to a good old-fashioned cover-up to preserve power and avoid scandal and accountability.”

“There is an ugly clericalism on full display in this present matter, the type of which Pope Francis is trying to purge from the Church,” he continued. “Our bishops must be held accountable for their decisions, their behavior, and their performance. Our Catholic faithful deserve better and will demand better in the coming years.”

In a statement released earlier this week, Griffith said he stands by those words today.

“I welcome a thorough accounting of the matter,” he said.

Charles Collins and John L. Allen Jr. contributed to this report.

[Editor’s Note: This story has been updated to include comment from Mary Rice Hasson.]