CONCORD — A mother of a former Phillips Exeter Academy student told a jury Monday that it was her family’s dream come true when their son was accepted into the school.

The dream changed when a federal suit filed in late August by the boy’s parents alleged their son was wrongfully expelled after a sexual encounter with a female student of the same age.

In court Monday, the mother alleged the school did not follow proper protocol, while Phillips Exeter maintained consistency in dealings with her son

According to the suit, the boy, referred to as John Doe, was placed on leave and expected to attend therapy after administrators found out about the encounter, but his parents were told he could return to school this fall.

However, over the summer, the suit claims, administrators told the parents if the boy was not voluntarily withdrawn from the school, he would be involuntarily removed for sexual misconduct. The suit was originally filed by both the mother and father of John Doe. Father Doe recently died after a long battle with cancer.

In an opening statement, attorney Megan Deluhery, who represents the Does, described the January 2016 sexual encounter in which the female student, referred to as Jane Roe, got on top of John in a dormitory room and initiated a sexual act with her hands, the attorney said. After some confusion arose, John and Jane ended their encounter, she said. Both students were 15 years old at the time.

Jane went to the campus health center in February to detail the encounter, which led PEA to contact the Exeter Police Department and the Division of Children, Youth and Families because it involved a situation with minors under New Hampshire legal age of consent.

“(The Academy), to be charitable, mishandles the situation,” Deluhery said.

Deluhery introduced the E Book, which is the student handbook that is issued each year. In the book, a discipline committee process is outlined. The committee is made up of faculty and students who hear evidence in major and minor cases on campus. Deluhery argued that John Doe was never given the opportunity to go before the discipline committee.

Within a series of meetings between February and March, John Doe was made aware that he had been placed on dean’s leave for the spring trimester, although prior meetings had led him to believe he was not subject to disciplinary action. Findings of private investigator Kai McGintee, who was hired by the school to conduct an investigation, showed that while she had some concerns with John, there was no malice, forcible action or evidence of sexual assault. The Does say PEA told them that if John attended therapy and avoided talking about the situation on social media, he would be able to attend school again in the fall.

“He makes every effort to comply with the rules the dean’s leave gave him,” Deluhery said.

On June 22, John was essentially expelled, according to Deluhery. The Does disputed the decision for much of the summer.

On Aug. 16, the school released their final decision and told the Does, “Withdraw your child or we will withdraw him immediately,” Deluhery said.

Deluhery said when John was first placed on dean’s leave, he was given reason to believe he would be back at school. His belongings were stored on campus and he continued to receive the school's fall catalog and reminders for the fall term.

“This case is about the rules,” Deluhery said. “Exeter says John broke the rules. But ladies and gentlemen, Exeter broke the rules.”

Steven Richard, an attorney representing PEA, argued that Exeter is no different than schools facing these challenges nationally.

“This is a challenging matter,” he said. “It wasn’t an easy situation to respond to.”

Richard said the allegation that the media frenzy surrounding the school’s alleged mishandling of other sexual misconduct cases affected John Doe’s case was untrue.

Richard introduced the welcome page to the E Book, which states, “This document as written does not limit the authority of the Academy to alter its rules and procedures to suit any unusual or changed circumstances.”

Richard argued that John Doe’s case needed immediate attention.

“This isn’t a plagiarism case,” he said. “This is a non-standard situation.”

Richard also pointed out that in a March letter describing John Doe’s dean’s leave, the letter concluded with, “In June, the deans will review John Doe’s case and determine whether or not he is permitted to return to school next fall.” He said the Does were never given a promise that John would return to school, despite their claims.

It later came to light that Jane Roe had begun referring to John on campus as “a rapist.” Because of Jane’s comments, Richard said, the decision to remove John from school was also in part because it may not have been possible to reintegrate him back into the community.

“It’s noted on the transcript as a withdrawal, so it would give John the opportunity to thrive and move on,” he said.

John Doe and Mother Doe were cross-examined on Monday.

Many of Deluhery’s questions to John focused around his opinion of the 30-minute period in which he sat down with investigator McGintee. John called the interview unfair and bias.

“I felt that she wasn’t trying to hear my end of the story,” John said. “She would ask these closed questions that implied something about what Jane Roe previously told her.”

John alleged that at one point, McGintee laughed at him when he felt uncomfortable answering a question, even though faculty advisor Alex Myers. told him beforehand that he didn’t have to answer questions he didn’t want to.

John said he started crying when he found out he’d been placed on dean’s leave.

“I felt they were basing this on false evidence,” he said. “They didn’t have my side of the story, they just had hers.”

John wrote a detailed email to Melissa Mischke, PEA dean of students, attempting to clarify facts in the situation and make sure his side of the story was heard. In emails shown to the court, Mischke responded that she was “disappointed” that John had not offered such information sooner, but his words did not “negate their opinion.”

John said Mischke never followed up with him on the evidence that he put forth in emails.

Richard asked John if he’d ever considered going to Mischke to say he didn’t feel the investigation was fair, of if he ever requested a discipline committee hearing. He answered no to both.

Mother Doe argued on the stand that while she and her husband were told about the findings of the investigation broadly, they were never shown the actual investigation.

“Every time we talked to them, there was some new accusation,” she said.

The lawsuit seeks a refund of tuition and other school-related expenses, plus money for therapy, travel and unspecified damages for emotional distress, as well as John’s reinstatement at Phillips Exeter.

The trial continues Tuesday.