On Wednesday these Buffalo Catholics finally got their wish when the Vatican announced Pope Francis had accepted Malone's resignation. No reason was given for the resignation.
"The overwhelming emotion is relief that we don't have to hold signs that say Bishop Malone has to go," said Siobhan O'Connor, a former secretary to Malone who later became a whistleblower and accused the bishop of mishandling abuse cases.
O'Connor says she is disappointed, however, that the Vatican did not announce the reason for Malone's removal or the results of its investigation into the Buffalo Diocese.
"It's a reminder that transparency is far from reality in the church," O'Connor said.
Malone issued his own statement, attributing his early retirement to turmoil caused by the Catholic Church's clergy sexual abuse crisis, and discord over his response to it.
The Diocese of Buffalo "will be better served by a new bishop who perhaps is better able to bring about the reconciliation, healing and renewal that is so needed," he wrote in a letter released by the diocese.
"It is my honest assessment that I have accomplished as much as I am able to, and that there remain divisions and wounds that I am unable to bind and heal," said Malone in the letter.
All bishops are required to submit their resignation to the pope when they turn 75. Malone is 73.
Since the church's clergy sexual abuse crisis reignited in 2018, bishops across the country have come under greater scrutiny for the crimes and cover ups alleged to have occurred on their watch. Few faced louder and more persistent accusations than Malone, who had led the diocese of some 600,000 Catholics since 2012.
In October, the Vatican announced its own investigation -- called an Apostolic Visitation -- into the Buffalo diocese. The results of that probe have not been made public. But the Vatican has a final report, and Malone submitted his resignation to Pope Francis last month, after Malone was made aware of the results, the Vatican's embassy in Washington said.
Malone asked for early retirement when he was in Rome with a contingent of bishops from the United States as part of regularly scheduled "ad limina" meetings with the Pope, the embassy in Washington said.
A spokeswoman told CNN the list Malone released included only priests accused of abusing minors, not those accused of misconduct with adults.
Later, the diocese revised its list of credibly accused priests from 42 to 78.
Still, Malone adamantly resisted calls for his resignation, even when prominent local Catholics and some of his own priests called for his ouster, insisting that a "shepherd does not desert the flock."
"Buffalo is a microcosm of the current US clergy abuse crisis and a cautionary tale," said Terence McKiernan of the watchdog group Bishop Accountability.
"While the drama of Malone's incomplete list of accused priests has played out in Buffalo, 100 other U.S. bishops have released lists of their own."
Malone is the fifth US bishop to resign or retire since the latest outbreak of allegations in the church's sex abuse scandal began last summer, according to Bishop Accountability.
Malone said he anticipated people would surmise his resignation stems from the Vatican's investigation, he wrote in Wednesday's letter.
"While I was made aware of the general conclusions of the report, which were a factor in my discernment, my decision to retire early was made freely and voluntarily," he wrote.
In Malone's stead, Edward Scharfenberger, the bishop of Albany, will temporarily lead the Buffalo diocese, the Vatican announced.
At a press conference Wednesday, Scharfenberger said he plans to spend one day each week in Buffalo.
"I am here for you. I am here to listen to you. I am here to walk with you and I am here to help you heal," the bishop said. "And I would prefer to convey that message by what I do and not just what I say."
Correction: This story has been updated with the correct amount abuse survivors received from the victim's compensation fund.
CNN's Rosa Flores, Joe Sutton and Jason Hanna contributed to this report.