Archbishop John Nienstedt resigned Monday, closing a troubled chapter in the history of the Catholic Church in the Twin Cities.

After two years of revelations about the failure of the Archdiocese of St. Paul and Minneapolis to protect children from sexual abuse at the hands of priests, Minnesotans awoke to the news that Pope Francis had taken action at last. A statement from the Vatican said the pope had accepted the resignations of both Nienstedt and Auxiliary Bishop Lee Piche.

A letter from Nienstedt on the archdiocese website admitted to no mistakes, but said that his leadership "has unfortunately drawn attention away from the good works" of the church. "Thus, my decision to step down."

"I leave with a clear conscience knowing that my team and I have put in place solid protocols to ensure the protection of minors and vulnerable adults," Nienstedt wrote.

Piche's statement was briefer. "The people of the Archdiocese of Saint Paul and Minneapolis need healing and hope. I was getting in the way of that, and so I had to resign," he wrote. "I submitted my resignation willingly, after consultation with others in and outside the Archdiocese."

Former priest Curtis Wehmeyer Minnesota Department of Corrections

The resignations came weeks after prosecutors in St. Paul filed criminal charges against the archdiocese for its "role in failing to protect children and contribution to the unspeakable harm" done to three sexual abuse victims of former priest Curtis Wehmeyer, now serving a five-year prison sentence for molesting two boys. He faces prosecution involving a third boy in Wisconsin.

Prosecutors said church leaders had failed to respond to "numerous and repeated reports of troubling conduct" by Wehmeyer, from the time he entered seminary until he was removed from the priesthood in 2015. The criminal complaint says many people — including parishioners, fellow priests and parish staff — spoke out about Wehmeyer, but in vain. No individual was charged.

Ramsey County Attorney John Choi, left, and St. Paul Police Chief Tom Smith announced criminal charges against the archdiocese June 5 in St. Paul. Jennifer Simonson | MPR News

"While today's resignation will be viewed as a positive development by many in our community, the pending criminal action and civil petition and the ongoing investigation will continue," said Ramsey County Attorney John Choi.

"Today's resignations do not directly accomplish those goals," he added, "but I believe that it is an affirmative step toward a new beginning and much needed reconciliation."

A woman whose sons were among Wehmeyer's victims described herself as "very relieved" at the news of the resignations. "This has been a long time coming," she said. "Actually, I'm still hoping criminal charges will be brought."

She said her boys, raised with television shows like "Law & Order," have come to expect quick resolution of criminal cases. "For them to be waiting 20 months or three years, it's been just tedious for them," she said. Now, she added, the boys have learned that "yes, people are going to be held accountable."

It seemed "sort of pitiful to me that it took the formal charges against the archdiocese for them to reflect on the fact that they haven't aided in the healing" her family needs, she said.

Explore the full investigation Clergy abuse, cover-up and crisis in the Twin Cities Catholic church

Other players in the long drama expressed relief as well.

Jennifer Haselberger, the former top canon lawyer whose revelations first rocked the archdiocese two years ago, said she thinks Nienstedt's resignation is a "very good sign" that the cover-up is over.

"If the blame for it lies with anyone," she said of the resignations, "it lies with the two men themselves."

Attorney Jeff Anderson, who represents people who have filed abuse claims against the archdiocese, said that civil cases will still proceed, but that the resignations are an important symbolic gesture to victims of clergy abuse.

"It does come with some sense of relief, because he does represent, as head of the archdiocese, the focal point of the longstanding problem," Anderson said. "But it's also important for everyone to realize that this whole problem is not about one man, even though he was at the top. It's about the system and all those that have been part of it.

"This resignation signals to all of us that there is now some change being pressured at the top in a way it has never been before, and that brings promise for real change from the top on down."

Bernard Hebda in Newark, N.J., in September 2013. Associated Press | File 2013

The Vatican named Archbishop Bernard Hebda, who is set to lead the Archdiocese of Newark, N.J., in 2016, to fill in temporarily as apostolic administrator for the Twin Cities.

In a letter to Twin Cities Catholics, Hebda made clear that his role will be not only temporary but part-time. "[I]t is my intention to be as available as possible, while still fulfilling my responsibilities as the coadjutor archbishop of Newark," he wrote.

Pope Francis appointed Hebda to the New Jersey post in 2013. Hebda will serve alongside the current archbishop until July 2016, and then take over upon the retirement of his predecessor. Jim Goodness, spokesman for the Archdiocese of Newark, said that Hebda "now has two full-time/part-time or two part-time/full-time positions."

At midday Monday, Auxiliary Bishop Andrew Cozzens made a brief statement to reporters across the street from the St. Paul Cathedral.

"There will be many unanswered questions as we take this significant transitional step to new leadership," Cozzens said. "I pledge to you personally, though, that Archbishop Hebda and I will work closely to bring our archdiocese into a new day."

Cozzens took no questions.

The resignations came just days after Pope Francis, who is planning to visit the United States this fall, approved the creation of a tribunal inside the Vatican to hear cases of bishops who failed to protect children from sexually abusive priests.

That action followed years of criticism that the Vatican had never held bishops accountable for having ignored warnings about abusive priests and simply moved them from parish to parish rather than report them to police or remove them from ministry.

Nienstedt's departure makes him one of only a few American bishops to resign as the result of a clergy sex abuse scandal. In April, Pope Francis accepted the resignation of Kansas City Bishop Robert Finn, who had been convicted of failing to report a suspected child abuser. Boston's Cardinal Bernard Law resigned in 2002 after the clergy sex abuse scandal exploded in his archdiocese.

Nienstedt's turbulent tenure

When Nienstedt arrived in the Twin Cities in 2007, he said his priority as archbishop would be unity.

"I wanted to spend my time as being a bishop building up the unity of the church, building unity between churches, and then building a sense of harmony in the world," he explained in a 2010 interview.

Instead, he presided over one of the most turbulent and divisive periods in the diocese's 165-year history.

Nienstedt rose quickly through the Roman Catholic hierarchy — serving as a secretary to the archbishop of Detroit and rector of Sacred Heart Seminary. He was known as a stickler for rules, someone who embraced the Catholic Church's teachings on abortion and same-sex marriage.

He fit in well in the conservative eras of Pope John Paul II and Pope Benedict. In 2001, Pope John Paul II appointed him to serve as the bishop of New Ulm, Minn.

Nienstedt became a hero to some Catholics and an embarrassment to others. He urged parishioners not to see the movie "Brokeback Mountain." But his conservative approach reflected the mood at the Vatican at the time, and in 2007, Pope Benedict selected him to serve as the new archbishop of St. Paul and Minneapolis. There, he helped initiate and promote an unsuccessful campaign to ban gay marriage in Minnesota.

When Nienstedt arrived in the Twin Cities, the archdiocese was already decades into a cover-up of clergy sex abuse. His predecessor — Archbishop Harry Flynn — had even cut secret deals with some abusers.

Betrayed by Silence: The investigation in four chapters

As MPR News began investigating the church's handling of abuse claims, and attorneys began preparing dozens of lawsuits, Nienstedt found himself at the center of a growing scandal.

The crisis began in the fall of 2013 when MPR News revealed that Nienstedt had authorized secret payments to priests who had sexually abused children, did not report alleged sex crimes to police and failed to warn parishioners about Wehmeyer's sexual misconduct.

Auxiliary Bishop Lee Piche spoke to participants in a rosary procession on the steps of the Capitol in May 2012. Alex Kolyer for MPR News 2012

The fallout was immediate. Nienstedt's top deputy resigned within days. Priests met with Nienstedt privately and urged him to resign. Nienstedt refused. Almost no one — priest or parishioner — came to the archbishop's defense in any meaningful way.

At a private meeting, priests confronted Nienstedt about his decision to cover up abuse. In a secret recording obtained by MPR News, a priest can be heard shouting at Nienstedt: "Archbishop, you're a liar, you're a thief. You're a coward."

Priests were particularly angry with Nienstedt for his silence — which left them having to explain to parishioners why he had protected priests accused of sexually assaulting children.

Nienstedt publicly admitted mistakes had been made. The archbishop named a task force that cited poor oversight and flawed policies in the handling of abuse allegations.

He also faced allegations of his own. Three months after the scandal broke, police opened a criminal investigation into a claim that Nienstedt had touched a boy inappropriately. At the same time, Nienstedt secretly authorized a law firm to investigate his private life. Haselberger, the archdiocese's former top canon lawyer, was due Monday to speak to Ramsey County prosecutors about what she had told the lawyers conducting that investigation.

Nienstedt was never criminally charged. He voluntarily "stepped aside from all public ministry" during the police investigation. He denied the allegations against him and announced the following March that he had returned to public ministry.

By then, calls for his resignation among parishioners and the public had grown.

Archbishop John Nienstedt at a press conference Friday, Jan. 16, 2015, in St. Paul, discussing the archdiocese bankruptcy filing. Jeffrey Thompson | MPR News

As the crisis deepened, Nienstedt remained largely out of the public eye. He waited eight months to grant his first interviews on the abuse scandal. In July of 2014, he told MPR News that he had been caught off guard by its reporting.

Nienstedt said he trusted others when they told him the abuse problem was in the past. "I, in a sense, didn't see the forest for the trees," he said. "I was aware of certain problems with misconduct on the part of different priests on a day-to-day basis, but I didn't get the overall picture of where we stood."

Behind the scenes, as dozens of victims came forward, the archdiocese's attorneys plotted a course that would end in bankruptcy. In January, at a news conference to announce the bankruptcy filing, Nienstedt insisted he had no intention of resigning. He compared his relationship with the archdiocese to a marriage:

"We all know that marriages go through rough difficulties and rough times, and this is one of those times," he said. "And it's seven years, and that's usually when it happens in marriage."

MPR News reporter Laura Yuen contributed to this report.