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BATTLE CREEK, Mich. -- Two weeks after he arrived in Battle Creek, Mich., to help an old friend with pastoral duties, former Twin Cities Archbishop John Nienstedt has left amid a swirl of criticism.

“After discussions with the archbishop conveying the expressed concerns by the faithful people of our community, he offered to withdraw from the diocese and I agreed,” the Rev. John Fleckenstein wrote in a letter to parishioners Thursday. “Archbishop Nienstedt has a deep concern for the church, and in light of the unintended discord that his presence was causing, he decided that this would be the best course of action so the church can remain focused on its mission.”

Nienstedt, who became archbishop of the Archdiocese of St. Paul and Minneapolis in 2008, had been a controversial figure leading up to his resignation in June of last year.

He had come under fire for his stance on gay marriage and his refusal to step down after a whistleblower said in 2013 that he and other top brass had played a role in protecting credibly accused predatory priests.

He resigned 10 days after the Ramsey County attorney’s office filed criminal charges against the archdiocese, saying church leadership failed to protect children by covering up for a sexually abusive priest now in prison. Nienstedt and Auxiliary Bishop Lee Anthony Piche resigned simultaneously.

Nienstedt had also been the center of a separate investigation, which he commissioned in 2014 to clear his name, after allegations that he’d had inappropriate sexual relationships with men. He has denied those allegations, though results of the probe have yet to be publicly released.

Attorneys for the law firm Greene Espel said their investigation was completed in August 2014. In June 2015, shortly after Nienstedt’s resignation, Minnesota Public Radio published a report saying the archdiocese had interfered with the investigation when it appeared the results would not have the intended result of vindicating the archbishop.

Also under Nienstedt’s watch, the archdiocese filed for Chapter 11 bankruptcy, citing an operating deficit and mounting clergy sexual abuse lawsuits.

It wasn’t long after his move to Michigan that his controversial past caught up with him.

Nienstedt traveled to Battle Creek on Jan. 6 to help out as an assistant pastor at St. Philip Roman Catholic Church, part of the Diocese of Kalamazoo.

The pastor there, Fleckenstein, announced Nienstedt’s arrival in a church bulletin, saying that he’s known Nienstedt for about 20 years and that Nienstedt would stay for about six months while Fleckenstein dealt with medical issues.

After media reports surfaced days after Nienstedt’s quiet move to the Michigan parish, the Diocese of Kalamazoo sent a letter to parents of a Catholic school there to address “recent concerns expressed regarding Archbishop John C. Nienstedt’s temporary stay in the diocese.”

Nienstedt “voluntarily offered his assistance” and “has not been appointed, assigned or ‘hired’ by the diocese,” the letter said. Nienstedt was considered “a priest in good standing,” but was not “scheduled” for any interactions with schools.

The letter, signed by the Vicar General, Msgr. Michael Osborn, said, “We regret that this important information was not more widely distributed, as was originally intended.”

The backlash was immediate from parishioners who criticized church leaders for bringing in the archbishop.

In an letter published by the Battle Creek Enquirer last week, a parishioner and mother wrote of her concerns and excoriated Kalamazoo diocesan leaders for green-lighting Nienstedt’s move.

“You urge ‘reason and charity,’ as though we’re expressing unfounded or mild concerns, as though there is no evidence or information to warrant caution,” Samantha Pearl’s letter said. “Let us be honest, Bishop (Paul) Bradley, your permission to allow this to happen, despite the repeated and egregious failure of Archbishop Nienstedt to protect children, suggests you place the protection of this man and his reputation above the protection of our children.”

Diocese Bishop Paul Bradley issued a letter Thursday, apologizing for the ordeal.

“Archbishop Nienstedt’s presence has unintentionally brought about a sense of disunity, fear, and hurt to many of you during this brief period of time,” Bradley wrote. “As your spiritual father and shepherd, I regret that more than words can express. While I made every effort to ensure that there were no canonical restrictions regarding the exercise of Archbishop Nienstedt’s priestly ministry at St. Philip Parish, I should have foreseen the full impact and strong emotional reaction to his presence in the Diocese.”

Nienstedt did not respond to a request for comment Thursday.