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First, a whistleblower revealed that Bishop Richard J. Malone of Buffalo, N.Y., had kept files about abusive priests that he hid from the public. Then leaked recordings showed that he was reluctant to remove a parish priest whom he called a “sick puppy.”

On Wednesday, after months of pressure from priests and lay leaders, the Vatican said in a statement that it had accepted the resignation of Malone, effective immediately.

While the statement from Rome did not specify a reason behind the resignation, a second statement, from the Vatican’s office in Washington, D.C., made clear that Malone had asked to retire early after being told the results of a Vatican investigation into his handling of the clergy sex abuse crisis.

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Malone, in a letter to the diocese, said he had made the decision to step down “freely and voluntarily” after being made aware of the conclusions the investigation.

Malone, 73, had steadfastly maintained that he was doing well in the diocese, and said in September that he did not think he should resign. Among many Catholics in Buffalo, where Malone was approaching persona non grata status as the scandals continued, there was a palpable sense of relief this week that the Vatican investigation appeared to have forced him to reconsider.

The diocese has seen a steady exodus from the pews and a decline in donations, local Catholics said. A poll conducted by The Buffalo News in September showed that 86 percent of local Catholics wanted Malone gone.

“For better or worse, he had become the lightning rod for all that was wrong, and we really weren’t going to make any progress toward healing and reconciliation as long as he remained,” said John J. Hurley, the president of Canisius College, who was part of a lay group, the Movement to Restore Trust, that had called for Malone’s removal. “People are hopeful that we are turning the page and looking forward to a new day.”

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But the Buffalo Diocese’s troubles are far from over. It is facing more than 200 child sex abuse lawsuits under the Child Victims Act, and is under investigation by both the Federal Bureau of Investigation and the New York attorney general for its handling of abusive priests over decades.

The bishop of Albany, Edward B. Scharfenberger, will be the temporary administrator of the diocese, the Vatican said.

In the past few years, Scharfenberger has gained a reputation for taking a more empathetic approach in his handling of the abuse crisis, and he has called for deeper involvement by the laity to help the church move forward.

“I will be doing a lot of listening and learning,” he said in a statement announcing his appointment, which he will hold alongside his current role.

Malone’s resignation was first reported on Monday by Whispers in the Loggia, a blog run by Rocco Palmo, a church analyst. He called Malone’s resignation “reluctant at best.”

Perhaps no bishop in America had been buffeted by scandal in the last two years more than Malone.

The Buffalo Diocese, one of the Northeast’s largest, with 600,000 Catholics, had been relatively insulated from the abuse scandals until 2018. Then abuse survivors began speaking publicly, and the local news media began to investigate, finding that at least some of the accused priests were still in the pulpit.

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Responding to pressure, in March 2018 Malone released a list of 42 priests accused of abuse over decades. But Siobhan O’Connor, who worked in the bishop’s office, had seen 117 names on a draft list in the diocese’s secret files. She began photocopying and then leaking the documents to WKBW, the local ABC affiliate.

The leaks revealed Malone, who had led the diocese since 2012, as clinical and protective in his dealings with church lawyers about abuse, seeking to limit disclosure of church secrets to minimize their damage.

“We did not remove him from ministry despite full knowledge of the case, and so including him on list might require explanation,” lawyers wrote to Malone about one priest, accused of having sex with a teenager, who was not included. Malone decided to leave that priest off.

“People were so frustrated and angry at Bishop Malone that they were losing their faith over it,” said O’Connor, who left her job and is now an advocate for abuse victims. His resignation, she said “is a sign for people that change can happen.”