Confronted with a lawsuit that made the accusations public, Baker killed himself in 2013, at age 62, in the monastery where he lived. On Monday, state prosecutors announced that three men who supervised him — Brothers Anthony M. Criscitelli, 61, Robert J. D’Aversa, 69, and Giles A. Schinelli, 73 — are each charged with one count of endangering the welfare of children and one count of criminal conspiracy.

“These men knew there was a child predator in their organization. Yet they continued to put him in positions where he had countless opportunities to prey upon children,” Pennsylvania Attorney General Kathleen Kane said in a statement. “Their silence resulted in immeasurable pain and suffering for so many victims. These men turned a blind eye to the innocent children they were trusted to protect.”

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Kane’s office also conducted an investigation into the Altoona-Johnstown Diocese in Pennsylvania which produced a damning grand jury report earlier this month. That report chronicled alleged abuses committed by 35 priests, dating to the 1950s, in wrenching detail. But it did not recommend charges against anyone. Most of the priests named in the report have died, and the statute of limitations has expired in some cases.

But when the grand jury turned its attention to friars based in Hollidaysburg, Pa. — the Franciscan Friars, Third Order Regulars, Province of the Immaculate Conception — it found cause to charge three men who served in the same job in the organization, that of minister provincial. The minister provincial controls which friar works where, prosecutors said. So Criscitelli, D’Aversa and Schinelli were the ones who placed Baker in the jobs which he allegedly used as opportunities to molest children, for years.

Marci Hamilton, a constitutional law scholar at Yeshiva University and prominent attorney for child sex abuse survivors, said that the Pennsylvania attorney general’s decision to charge men who supervised abusers is rare.

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“What we’re seeing is the incremental improvement in the way in which prosecutors are seeing these issues and dealing with them. This sends a real message of support to the victims, not just of Stephen Baker but across the country,” Hamilton said.

She said supervisors have only previously been charged with child endangerment in Catholic church cases three times anywhere in the country. The first case, also in Pennsylvania, led to a Philadelphia priest’s conviction in 2012. That case set an important precedent in Pennsylvania, Hamilton said: “The supervisor does not have to have direct contact with children to be found responsible for their welfare.”

Hamilton noted that Monday’s charges are also the first such charges in the country to target a religious order. Orders like the Franciscans are notoriously secretive, and the worldwide regularity among monasteries of the order might help prosecutors elsewhere to bring cases similar to the Pennsylvania one, she said.

“This is groundbreaking. We have not seen a prosecutor charge an order of priests,” Hamilton said.

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The Franciscan order released a statement that said:

We are deeply saddened by the news released today by the Pennsylvania Office of Attorney General. With compassion for the victims and their families, as well as for the Catholic family and the community at large, the Province and its leadership have worked to cooperate with the Office of Attorney General throughout this investigation in the hope that this information could shed light on events that the Province, too, struggles to understand. The Province extends its most sincere apologies to the victims and to the communities who have been harmed. It invites the community to join it in prayer for healing and understanding, and for all the priests and brothers who honor their vocations and the Church.

Before Baker died, the Franciscans settled a lawsuit with 11 victims who said Baker abused them in the 1980s and 1990s when he worked at a school in Ohio, according to the Pittsburgh Post-Gazette. That settlement prompted 25 students from Bishop McCort Catholic High School in Johnstown, Pa., where Baker taught from 1992 to 2000, to say they had also been abused by him.

Now, the grand jury said, more than 80 Bishop McCort students have said they were victimized by Baker. Prosecutors said that Baker repeatedly said he was treating boys as an athletic trainer, which he was not trained to do. Then he would grope their genitals and penetrate them with his finger.

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Prosecutors pointed to repeated chances that the friars had to stop Baker: Schinelli sent Baker for a psychological evaluation and got back the answer that Baker should not have contact with children; then Schinelli assigned Baker to Bishop McCort.

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D’Aversa found an accusation of sexual abuse credible in 2000. He removed Baker from the school, then put him in charge of overnight youth retreats around the country. Prosecutors said D’Aversa knew that Baker volunteered at Mt. Aloysius College and that he assigned Baker to a church bingo program, where the grand jury found that he again abused minors.

Criscitelli let Baker work in a shopping mall, again around children, prosecutors said.

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Correction: An earlier version of this story referred to St. Aloysius College. It is Mt. Aloysius College.