Navy Cmdr. Aaron Rugh at the 2015 ceremony in which he became a judge for the Navy-Marine Corps Court of Criminal Appeals. (Natalie Morehouse/U.S. Navy photo)

The three officers instructed to decide whether Maj. Mark Thompson should be expelled from the Marine Corps for sexual misconduct had just heard opening arguments when the government called its first witness.

Aaron Rugh was the U.S. Navy commander who had led the prosecution against Thompson at a court-martial 10 months earlier. He would testify by phone.

“Before this witness is called, I would like a proffer of relevancy,” complained Maj. Joseph Grimm, Thompson’s attorney. “It is highly unusual for a former prosecutor to testify in a case like this.”

Thompson had been accused of having sex with two female students he knew through the rifle team at the U.S. Naval Academy, where he taught history. At his 2013 court-martial, Thompson was acquitted of a rape charge but convicted of five lesser crimes. In March 2014, after serving two months in a military brig, he faced what is known as a board of inquiry, which would determine whether he should be kicked out of the Corps.

What Rugh — now a judge on the Navy-Marine Corps Court of Criminal Appeals — told them that day has since come under intense scrutiny, which could lead to an internal investigation and potentially serious consequences.

Maj. Mark Thompson, who was convicted of sexual misconduct in a case involving two female students, at the U.S. Naval Academy, where he was a history teacher. (Nikki Kahn/The Washington Post)

He testified that government authorities had interviewed family members of Sarah Stadler, one of the two accusers, about a key night in the case — a claim Stadler’s mother and brother vehemently denied to The Washington Post.

The Office of the Judge Advocate General of the Navy wouldn’t allow Rugh to be interviewed, and a spokeswoman has repeatedly declined to discuss the case because it is under appeal. But she strongly defended the judge Thursday.

“Commander Rugh strenuously denies the allegation that he was untruthful during the board of inquiry,” Jennifer Zeldis said. “He has a strong reputation for integrity and fair dealing as a prosecutor, defense counsel and military judge.”

In January, when The Post first informed the military that Rugh had been accused of lying under oath, Zeldis said Rugh’s testimony before the board “was accurate to the best of his recollection at the time.”

But he also made at least two other statements at the hearing that are now being challenged — one related to the location of witnesses at the court-martial, and another that referred to the nature of the text messages between Stadler and Thompson.

Rugh acknowledged to the board that he had not reviewed the case file before testifying.

“It’s troubling that Cmdr. Rugh was, in the kindest light, seemingly negligent when he made apparently false statements under oath at Thompson’s administrative board,” Rachel VanLandingham, a former U.S. Air Force judge advocate, said in an email. “If true, such recklessness brings into question his fitness as a judge on the military court of criminal appeals on which he is sitting, and I’m confident the Judge Advocate General of the Navy, who has a stellar record of integrity, will investigate appropriately.”

After a flawed sexual assault investigation, a Naval Academy instructor tries to prove he has done nothing wrong. But did he? (Ashleigh Joplin/The Washington Post)

Why Rugh testified in the first place has also raised questions. Four military law experts told The Post that prosecutors almost never do that.

“In my own experience, I can’t think of a time that I’ve seen it happen,” said Christian L. Reismeier, a retired rear admiral who served as chief judge of the Navy during his 31-year military career. “There’s nothing that prohibits it. It’s just unusual.”

According to the testimony, Rugh wanted to address an aspect of the case not presented to the court-martial jury.

Stadler had alleged that she and Thompson had consensual sex about seven times over four months in 2011 — including once when they were joined by a male friend of his, also a Marine. During the trial, she spotted that Marine, whose name she had forgotten. He was at the Washington Navy Yard to testify on Thompson’s behalf.

Rugh explained to the board how Stadler had made the identification. The Naval Criminal Investigative Service later confronted the other officer, but he invoked his right to remain silent, and the query ended.

Rugh’s decision to testify, though, opened him to questions from both the defense attorneys and the three board members, who didn’t hide their skepticism of Thompson’s conviction.

They repeatedly pushed Rugh to describe the evidence that had proved Thompson’s guilt.

One member, Col. Sekou S. Karega, specifically pressed him about the evening of Stadler’s graduation. Stadler had testified that she and Thompson had sex that night for a final time before she left Annapolis to start her career as an officer. (After being reached by The Post earlier this year, Stadler discovered her old cellphone, which revealed that she and Thompson had seen each other the night after her graduation.)

Rugh told the board that Stadler’s “family, her brother, et cetera” had “verified” that she had been with them at their rental house on graduation night before leaving, then returning later.

But in an interview with The Post, Stadler’s mother, Laurel, called the former prosecutor’s statement “a complete and total lie.” She and her son denied that they had ever spoken to investigators about the case.

Both Stadler and the woman who had alleged that Thompson raped her said they were never notified about the board of inquiry, which allowed him to remain a Marine and also protested his conviction.

Stadler recently read a transcript of the hearing and said that Rugh told members something else that was inaccurate.

At the court-martial, most of the government witnesses stayed in one general room while they waited to be called, Rugh testified. But he said that the two women were placed “in an entirely separate witness room because of some of the discomfort or embarrassment for them.”

That wasn’t true, said Stadler, who recalled being placed in a small room along with the other government witnesses throughout most of the trial. Two of those people confirmed to The Post that she was there with them.

“It was awkward,” she said. “You’re sitting there just feeling judged.”

Stadler said she twice spent time alone in another room: Once when she reviewed her old statements just before taking the stand and again later in the proceedings so she could make travel plans to leave the District.

During his testimony, Rugh was also asked if it was possible that the text messages between Stadler and Thompson were related to the rifle team and not a sexual relationship. At the time, none of the texts between them had been found.

Rugh repeatedly denied that they could have been, testifying “that it is impossible within any kind of reasonable possibility that those text messages had anything to do with the shooting team.”

But, The Post has since discovered, some of them did have to do with the shooting team — and other topics entirely unrelated to a sexual relationship.

Many of the more than 650 texts, however, did strongly imply that Stadler and Thompson were involved in an inappropriate relationship — directly contradicting Thompson’s own sworn testimony to the board.

Thompson’s criminal convictions remain under appeal. Rugh, who now sits on the appellate court that will consider Thompson’s case, won’t be involved because of his role at the court-martial. But military justice experts say that the allegations against Rugh are significant.

“Professional misconduct by a judge advocate can lead to suspension or revocation of the right to practice, and for a sitting judge could lead to removal for cause if the charge is proven,” Eugene Fidell, who teaches at Yale Law School, said in an email. “A mere memory lapse could be asserted by the prosecutor, but he would have to explain under oath if an investigation is conducted.”