Malone also removed Biernat from his position as chaplain to a Carmelite monastery and prohibited him from residing in the bishop's residence in Buffalo.
The decree was signed on December 3, 2019, the day before Pope Francis accepted Malone's resignation, making it one of Malone's last acts as bishop of the diocese.
It is not clear if Malone imposed the penalties after a required canonical process, in which Biernat would have been able to defend himself, or if the bishop sought instead to issue the decree summarily before he was himself removed from office.
The decree refers to the apparent punishments variously as "penal remedies," "penal precepts," and "penances," although those terms have distinct meanings in canon law. The permanent deprivation of office, as imposed in the decree, is an "expiatory penalty" in the Code of Canon Law and not a precept or penance.
In the 18 months prior to his departure from office, Bishop Malone was the subject of successive scandals.
In November 2018, a former Buffalo chancery employee leaked confidential diocesan documents related to the handling of claims of clerical sexual abuse. The documents were widely reported to suggest Malone had covered-up some claims of sexual abuse, an allegation the bishop denied.
Six months later, in April 2019, Malone apologized for his handling of some cases in the diocese, and said he would work to restore trust. The bishop particularly apologized for his 2015 support of Fr. Art Smith, a priest who had faced repeated allegations of abuse and misconduct with minors.
"Lessons have been learned," Malone said in April.
In August 2019, a RICO lawsuit was filed against the diocese and the bishop, alleging that the response of the diocese was comparable to an organized crime syndicate.
The following month, Biernat took recordings he had made of meetings with Malone to WKBW in Buffalo.
Just days after the taped conversations were made public in early September, Biernat revealed that he himself had been abused by a diocesan priest while a seminarian.
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In an interview with local news station WKBW, Biernat said that in 2003, he was sexually assaulted by Fr. Art Smith at a rectory St. Thomas Aquinas parish in Buffalo. When Biernat went to then-auxiliary bishop Edward Grosz with the allegations, Grosz allegedly blamed him for not locking the door, and threatened his vocation if he did not keep silent about it.
Fr. Smith was eventually the subject of a letter from Bishop Malone to Vatican officials in 2015, where Malone asked that he be kept in ministry. In the same letter, Malone admitted that Smith had groomed a young boy, was accused of inappropriate touching of at least four young men, and had refused to stay in a treatment center. Smith was suspended from ministry in 2018 after a new abuse allegation against him was substantiated.
Malone was removed from office when Pope Francis accepted his resignation two years ahead of the canonical retirement age of 75.
He presented his resignation after the Apostolic Nunciature in Washington, D.C., announced in October that Bishop Nicholas DiMarzio of Brooklyn had been asked to lead an apostolic visitation and canonical inspection of the Buffalo diocese on behalf of the Vatican Congregation for Bishops.
That review concluded at the end of October, with DiMarzio having made three trips to Buffalo, and interviewing more than 80 people before submitting his report to Rome.
Malone said he had been made aware of the "general conclusions" of the report and the conclusions had factored into his discernment to resign, but that he had done so "freely and voluntarily."