A female supervisor at the Hawaii Preparatory Academy boy’s dormitory on the Big Island was having sex with a male student and officials didn’t do anything to stop her even though they knew or should have known it was happening, according to an independent investigation commissioned by the school.

The boy’s parents discovered the affair after reading text messages the faculty member sent to their son.

HPA Head of School Robert McKendry said in a written statement that the school made many changes to its policies, practices and procedures to improve student safety after the dormitory supervisor Arati Clarry, who was also the school’s director of Alumni and Student Programs, was fired in March 2016 for having an inappropriate relationship with a 17-year-old student.

Still, there were lessons learned,” McKendry said.

The school revised protocols for residence halls, updated reporting procedures and implemented more extensive annual training on policies, appropriate boundaries between adults and students and how to report concerns of student sexual abuse, McKendry said.

The student with whom Clarry was having a relationship graduated from HPA last year. He was old enough to consent to sex under Hawaii law when Clarry was accused of having sex with him. The basis of the lawsuit is the family’s claim that HPA violated federal Fair Housing Act laws by failing to protect the student from the sexual harassment of a sexual predator. The student’s parents paid HPA to house their son in the dormitory.

Despite McKendry’s statement that she was fired, Clarry said in a written statement that she resigned to take responsibility for what happened and to protect her children, HPA students, and the school from what she felt was a “setup,” court documents show.

“I know unequivocally that I did not molest, abuse, sexually assault or rape anyone,” she said in her statement. The report, she said, gives her a sense of relief and vindication because it backs up her claim that she never forced the student to have sex.

The student and his parents sued the school this past May under the pseudonyms John Roe I, Jane Roe I and John Roe II. The parties reached a settlement last month after HPA was forced to turn over the investigation report.

The terms of the settlement are confidential but the family’s lawyers said in a court filing that during negotiations, HPA’s insurer made settlement offers of between $10,000 and $1.8 million. The family had asked for damages of at least $7.5 million.

Clarry said the student had often said that he wished he could win the lottery for his parents so they would have money and be happy. She said in court documents she believed she was the lottery ticket.

She lived in a faculty apartment with her minor children in HPA’s all-boys dormitory, even though the school has a general policy against housing single faculty members of the opposite sex in single-sex dormitories.

According to documents, HPA said it had trained all of its employees on appropriate boundaries with students. The training included a list of warning signs of a sexual predator — including having close, personal relationships with students; housing students in personal homes; going on trips and participating in extracurricular and overnight activities with students; transporting students in personal vehicles; “friending” students on social media; and departing from established procedures involving students.

The Roe parents said McKendry admitted having knowledge that Clarry, who was popular among students and alumni, exhibited warning signs but did nothing to protect their son, according to court documents.

They said Clarry formed a “posse” of male and female students to whom she gave special privileges, including taking them on surfing trips in her personal vehicle, giving them free access to her faculty apartment and letting them sleep there overnight. The parents claimed that McKendry was aware of concerns about Clarry relationships with students but didn’t do anything about it, documents show.

According to the investigation, HPA Dean of Students Fred Wawner told Clarry by email in February 2016 that students were not allowed to sleep in faculty houses, after learning that two female students signed out of their dormitory to spend the weekend at Clarry’s apartment.

In response to the email, Clarry said students had been allowed to sign out to her apartment the previous year.

The report said Wawner took no further action and HPA did not inspect Clarry’s apartment to see if students were sleeping there. School officials also did not review security video recorded by cameras inside the dormitory showing both male and female students going to Clarry’s apartment carrying blankets and pillows. It also shows the Roe student entering Clarry’s apartment late at night and leaving early the next morning.

Separate from the relationship with the Roe student, the report says school officials knew that Clarry let a young male HPA alumnus stay overnight in her apartment and Wawner had told Clarry doing so was “not a good idea.” Also, the report says, school officials knew that Clarry had sex with a second recent male graduate but didn’t investigate whether that relationship began when he was a student.

School officials also took no action after receiving reports that Clarry friended students on her Facebook page, posted pictures of shirtless male students in her apartment and a video of the Roe student, according to the report.

Other employees told the investigator that they saw Clarry touch and caress the Roe student on school- sponsored overnight trips to Kauai and Hawaii Volcanoes National Park and did nothing to stop Clarry from taking the Roe student in her personal vehicle for a one-on-one study session at night. Another employee said she saw the Roe student and Clarry sitting in the front seat of her car on campus kissing.

The employees shared their concerns with other employees but did not report what they saw to administrators for fear of retaliation.

The Roe parents claim that a tight-knit group of current and former administrators, including McKendry and Wawner, befriended Clarry, dismissed concerns and complaints about her as personal gripes and sour grapes, and told her when there were complaints about her — even when the complaints were made confidentially.

HPA announced in July that its board of trustees officially began searching for a new head of school to replace McKendry, who is leaving next year.

Clarry, 39, is a 1996 HPA graduate and was hired by her alma mater in 2010.

HPA reports that enrollment at its Waimea campus for the current school year is 626 in grades K-12. At $26,800, its high school tuition is the highest in Hawaii.

The school reported to the IRS that for the 2016 calendar year it had $38 million in gross receipts and $129 million in net assets.