Giles A. Schinelli, 73; Robert J. D'Aversa, 69; and Anthony M. Criscitelli, 61, each face charges of criminal conspiracy and endangering the welfare of children.
"These individuals knew that Brother Baker was a child predator and that Baker had faced allegations of child molestation," Pennsylvania Attorney General Kathleen G. Kane said. "These individuals did not report this knowledge to police."
Baker killed himself in 2013. He had not been charged beforehand. The state expanded its investigation to see whether anyone knew about Baker's risk to children and turned a blind eye to it.
Kane said a grand jury identified "significant wrongdoing" on the parts of Schinelli, D'Aversa and Criscitelli. All three are members of the Franciscan Friars, Third Order Regulars, Province of the Immaculate Conception, which is based in Blair County.
"They were more concerned with protecting the image of the order and more concerned with making sure they were in touch with lawyers rather than the flock that they served," Kane said.
The alleged conspiracy allowed Baker to sexually abuse more than 80 victims, the attorney general's office said.
Attorneys for Schinelli and Criscitelli did not immediately returns calls seeking comment.
Bob Ridge, who represents D'Aversa, declined to comment.
The alleged roles in the conspiracy
A grand jury found that order leaders knew about a 1988 sexual abuse allegation involving Baker, but still allowed him to work with children at Bishop McCort.
Schinelli, who served as minister provincial from 1986 to 1994, sent Baker for a psychological evaluation and was told Baker should not have one-on-one contact with children, the attorney general's office said.
Despite that, Schinelli later assigned Baker to Bishop McCort, where he had regular contact with children, the grand jury found. Baker worked at the school from 1992 to 2000, teaching religion and serving as an athletic trainer.
D'Aversa, the minister provincial from 1994 to 2002, removed Baker from the high school in 2000 after learning of a new allegation of child sexual abuse, Kane said. But he allegedly failed to tell school officials and police about the new allegation or why Baker was removed.
Instead, the attorney general said, D'Aversa later appointed Baker as vocations director for the Third Order Regulars -- a position that allowed Baker to conduct youth retreats across the country.
Criscitelli, the minister provincial from 2002 to 2010, also allowed Baker to come in contact with children by allowing him to work at a shopping mall, Kane said. According to the attorney general, Criscitelli knew Baker required "safety plans" that advised no contact with minors.
Allegations of groping students
Baker's role as an athletic trainer at Bishop McCort Catholic High School came despite having no formal training in sports medicine, Kane's office said.
Victims described incidents "involving Baker in which he would grope the genitals of male children and digitally penetrate their anuses," the attorney general's office said.
Even though Baker was removed from his school duties in 2000, he regularly returned to the school to participate in school activities and had access to school facilities until 2010, victims said, according to Kane's office.
In all, Baker was accused of molesting more than 80 children from Bishop McCort between 1992 and 2010. Many of the alleged offenses took place on school grounds or at a related training facility, the attorney general's office said.
But "the grand jury could not find conclusive evidence that the Bishop McCort administrators were aware of Brother Baker's history or of his sexually abusive conduct," Kane said.
Bishop McCort's board of trustees said it was pleased to learn of the charges against those accused of being complicit.
"Our goal always was and always will be the safety of God's children. From the beginning, this board has taken aggressive, proactive steps to investigate and address the disturbing actions of Brother Stephen Baker," the trustees said.
"We are pleased that the attorney general has decided to move forward and hold those complicit legally accountable, and we are committed to continuing to fully cooperate with law enforcement as this process continues. We pray that this is one more step on the path to helping the victims of Brother Baker reach peace and closure from this tragedy."
'Most sincere apologies'
Schinelli, D'Aversa and Criscitelli did not enter pleas during their arraignment this week, according to the Blair County District Court clerk's office.
Unsecured bail was set at $75,000 for each of them, meaning they did not have to post any money to be released. All three will remain supervised at their homes outside Pennsylvania.
Preliminary hearings for the three are set for April 14.
If convicted, each could face up to seven years in prison.
Attorney Thomas Farrell, who represents friars from the Province of the Immaculate Conception, said he was "deeply saddened" by news of the charges.
"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," he said.
"The Province extends its most sincere apologies to the victims and to the communities who have been harmed."
A nationwide message
Barbara Blaine, president of the Survivors Network of those Abused by Priests, said the charges send an important message.
"Those who commit clergy sex crimes are sometimes charged. But those who conceal those crimes are rarely charged," she said.
"We hope these charges will prompt more victims, witnesses and whistleblowers to come forward, call police, expose wrongdoers, protect kids and start healing."