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The head of a congregation of priests that owns St. Michael’s College School, the all-boys academy in Toronto plagued by allegations of assault and sexual assault by students, says he appreciates that the Catholic Church’s history of handling sexual misconduct will leave people “understandably skeptical” of the priests' ethics and transparency.

“There is a great deal of pain, sadness, confusion and shock,” Superior-General Kevin Storey of the Congregation of St. Basil, also known as the Basilian Fathers, said in an e-mail exchange with The Globe and Mail on Friday. It’s the first time he has spoken publicly about what he called the “shameful events” that allegedly occurred at the midtown private school.

What began as a police probe into a video, allegedly showing students sexually assaulting their peer with an object, has grown to police investigations into six incidents connected to the school. The other five include one other alleged sexual assault, three alleged assaults, including one with a belt and one alleged threatening incident. Six students have been arrested and charged with assault, gang sexual assault and sexual assault with a weapon, in connection to the first alleged sexual assault caught on video. Police were informed about that video by media inquiries, which came two days after principal Greg Reeves learned about the video.

“Please understand that it’s not appropriate for me to comment on or judge his decisions,” Father Storey said of Mr. Reeves, noting a police investigation is continuing and a committee is being struck to probe the school’s underlying culture. “When weighing what’s right in such terrible circumstances, we expect school leaders to put the safety and well-being of our students first, while fully complying with the law. The principal did what he thought was right: prioritizing communicating with the families, and quickly expelling the wrongdoers to protect the victims and all other students.”

Mr. Reeves, who resigned last week alongside former school president Jefferson Thompson, has said he had every intention of going to police had they not come to him first. The delay was in part to tell the victim’s family, but also to deal with the expulsion meetings he had planned. At least one arrested student was not among those expelled.

The Basilian Fathers currently make up the majority of the St. Michael’s board of directors. In the past three years, though, the board has added some lay members to their ranks, Father Storey said.

He’s been in “regular, informal” communication with board chair Michael Forsayeth since the grim news broke, but says there’s been no formal direction to the board from the General Council of the Basilian Fathers. They follow a principle of subsidiarity, which dictates that decisions are more effective at a local level.

The Basilian congregation is still dealing with the aftershocks of another sexual-assault crisis: the case of a priest named William Hodgson (Hod) Marshall. Father Marshall taught at St. Michael’s and several other schools, and was sentenced to two years in 2011 for the indecent assault of 16 children and one woman. There have been at least 17 lawsuits about his abuse, most settled out of court. According to evidence from one civil trial, Father Marshall told the church he had between 58 and 87 victims over three decades. He died at the age of 92 in 2014.

“The abhorrent actions of [Father] Hod Marshall, who taught at the school for three years in the 1950s, wreaked havoc on the lives of innocent children and decimated the church’s credibility,” Father Storey said. “The Basilian Fathers and the church as a whole have learned from this cross and shame that we bear.”

He listed new policies and procedures the congregation has implemented in the years since, such as psychological evaluations and independent review boards for new priests and an audit by child-safety specialists. “As dreadful as our past is, with extremely few clerical misconduct cases reported in the last 25 years, it appears that these policies are working,” he said. “Turning shameful events into an opportunity for learning and change is exactly what needs to happen at St. Michael’s today.”

He expressed optimism about broader changes potentially coming from the culture review.

“The first step is to understand the truth – no matter how hard it may be to hear.”