Marine Maj. Mark Thompson, left, was convicted of having sex with two female midshipmen while he taught at the U.S. Naval Academy. His friend, Marine Maj. Michael Pretus, right, is now being removed from his academy teaching position. (Left: Nikki Kahn/The Washington Post; Right: The Washington Post)

A second U.S. Naval Academy instructor has been implicated in a sexual misconduct scandal reverberating across a military still struggling to hold service members accountable when allegations are made against them.

The instructor, Marine Maj. ­Michael Pretus, is being removed from his position by Naval Academy leaders who said they weren’t aware of a former student’s sexual accusation against him.

The reassignment comes after a new investigation of a fellow ­Marine, Maj. Mark Thompson, who was convicted in 2013 of having sex with two female midshipmen while he was a teacher at the academy. In a stunning reversal, Pretus — a key defense witness at Thompson’s court-martial — has now agreed to testify against his longtime friend.

“I’m going to be a witness for the prosecution,” Pretus told The Washington Post in an interview Sunday.

Pretus, a decorated combat veteran, said that military authorities approached him after The Post’s revelations about Thompson’s case last month.

In 2005, Michael Pretus gets a tattoo from Brad Bellante at Spark Plug Tattoo in Fredericksburg, Va. The body art is in memory of several Marines who died while fighting with him in Fallujah. (Jahi Chikwendiu/The Washington Post)

[A Marine fights to prove he’s innocent of sexual misconduct. Then a lost cellphone is found.]

During Thompson’s 2013 trial at the Washington Navy Yard, Pretus challenged testimony given by Thompson’s accusers, Sarah Stadler and a younger classmate. Then, after being spotted by Stadler during the trial, Pretus himself was investigated for allegedly taking part in a threesome with her and Thompson in 2011. Under military law, an officer having sex with a midshipman is a crime, as is having a threesome.

The investigation, according to military records, ended after Pretus refused to cooperate. One year later, in 2014, the Marine Corps assigned him to teach history to midshipmen in Annapolis, where he has also served as a mentor to students who aspire to become Marines.

Officials at the Naval Academy, the Marine Corps, the Judge Advocate General of the Navy, the Naval Criminal Investigative Service and Pretus’s former command in New Orleans have been unable to explain how he taught at the academy for two years after being accused of having sex with a student.

Amid the embarrassing fallout, Cmdr. John Schofield, a Naval Academy spokesman, said that Pretus would no longer be allowed to remain in the classroom. The school, Schofield maintained, had “no knowledge” of the accusation against Pretus before The Post’s stories about Thompson.

“Under no circumstances would the Naval Academy have allowed for assignment on staff and faculty had there been disclosure of the circumstances and details of his involvement in that event,” Schofield said. “The Naval Academy immediately initiated administrative actions to reassign Major Pretus upon discovery of his past involvement with Major Thompson and Ms. Stadler.”

An NCIS spokesman said he didn’t know whether investigators had informed the academy of the investigation into Pretus but called it the responsibility of Pretus’s then-command, the Marine Corps Forces Reserve in New Orleans.

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)

A spokesman there acknowledged that the command knew about the investigation into Pretus but denied that it was the command’s job to inform the school of it.

“We wouldn’t have ever informed them because we didn’t have anything to do with the Naval Academy,” said spokesman Adam Bashaw. “We don’t select the next jobs.”

The new assignment, Bashaw said, would have been the duty of officials at Marine Corps Manpower and Reserve Affairs. That department said Pretus was “eligible” for the assignment but did not say whether officials there knew about the accusation against him.

A JAG spokeswoman declined to answer questions, referring them back to the Naval Academy. A spokesman for the Marine Corps, which is considering whether to bring new charges against Thompson, said officials there are working to determine the circumstances that led to Pretus’s assignment at the academy.

Stadler first learned that Pretus had become a teacher at the school when she was contacted by The Post in January.

“I was incredibly disgusted and discouraged,” she said this week, “because I just couldn’t believe someone who already broke laws and rules knowingly . . . was now working at an institution where he was supposed to interact and influence young midshipmen.”

[Military launches a new investigation into Marine’s sexual misconduct case]

The new investigation into Thompson — who was acquitted of rape but convicted of five other charges related to sexual misconduct three years ago — was launched after The Post reported on the contents of Stadler’s long-missing cellphone. Many of the more than 650 messages she and Thompson exchanged appear to contradict what he said under oath in 2014 to an administrative board that was deciding whether he should be expelled from the Marines. (Thompson, who has long denied any wrongdoing, did not respond to requests for comment for this report.)

A number of the texts also refer to a “Mike,” who Stadler says is Pretus. One exchange indicates that she went to Thompson’s home on a day when Pretus, according to his own statements to investigators, was staying with Thompson in Annapolis.

Asked by a reporter whether he’d ever had sex with Stadler, Pretus wouldn’t answer.

“I’m not going to comment on that,” said the 18-year veteran.

On Sunday, Pretus, who was scheduled to remain in the classroom one more year, said he was still teaching but did not know how his role in the investigation would affect his future there.

“It’s up in the air,” he said.

As of Monday evening, he was still listed on the Naval Academy’s website as one of the “Marine Company Mentors” to the school’s second battalion. On campus this weekend, his wood-framed photograph remained on display along with those of other members of the history department faculty. His office was packed with papers, photos and Marine Corps memorabilia.

On one poster, above the image of a Marine standing at attention, was a single word: “SERVE.”

Reconnecting after Iraq duty

The bond between Pretus and Thompson formed more than a decade ago as both men prepared for war after the Sept. 11, 2001, terrorist attacks.

They were assigned platoons on the same day: Thompson to sniper, Pretus to infantry. But when Thompson mentioned that he had extensive experience with that type of infantry platoon, a colonel switched their assignments.

“It ended up changing both of our lives,” Thompson testified at his administrative hearing.

Pretus fought in the Second Battle of Fallujah, where he lost two men during one of the military’s fiercest firefights since the Vietnam War.

The men reconnected at Quantico around 2005 and stayed close in the years after, a time when Pretus’s harrowing combat experiences defined much of his public life. At the time, The Post featured him in a story about service members getting tattoos to honor their slain comrades.

[Indelible memories for veterans of Iraq]

He gave gripping speeches about his experience, too. On Facebook, the officer frequently referred to the Marines he’d fought alongside and the burden he carried because of those who would never come home.

In April 2011, Pretus traveled to Annapolis to give a presentation on battlefield leadership to Thompson’s students.

It was during that trip, Stadler said in an interview, that she had sex with both men.

At 11:54 p.m. on April 26, 2011, she texted Thompson: “Thanks c u tomorrow for our run.”

“Schedule is good for 1600 run tomorrow,” he wrote back, using the military time for 4 p.m.

“Sounds good,” she responded.

They frequently used references to exercise, Stadler said, as a code for sex.

A few minutes later, Thompson continued: “Guest speaker tomorrow 4th 5th and 6th if you can stop by.”

“Where?”

“1st floor Sampson 115,” he wrote, referring to a classroom in the building that houses the history department. “I’ll be in the hallway.”

“Is it Mike?” she wrote. “Is that a smart idea?”

“Sure, there will be other guest. You won’t feel out of place.”

“I might stop by,” she responded at 12:31 a.m.

That “Mike,” Stadler said, was Pretus, who later testified at Thompson’s trial that he spoke to Thompson’s students the following day. She said that Thompson wanted her to see him.

“It was for me to get a look at him for the first time,” she said, “and give my thumbs up or thumbs down.”

Stadler approved, she said, and at 3:48 p.m. she texted Thompson.

“Still running at 1600?”

“Yes,” he wrote. “You?”

“Yeah about to leave my room.”

“Meet u at front or back?” she messaged him, referring to the two entrances at Thompson’s house.

“Front,” he told her.

“On my way,” she wrote at 4:01 that afternoon.

Two hours later, she sent him another message: “Best run ever! Thanks.”

Pretus refused to say whether he had seen Stadler that day.

Stadler and Pretus became friends on Facebook in 2011, The Post found, though it’s unclear how long they remained friends (they no longer are). Despite their former connection, Stadler maintains that she had forgotten his name by the time investigators contacted her in 2012.

A familiar face at trial

Stadler didn’t see Pretus again until she came to testify at Thompson’s 2013 court-martial in Washington, where she spotted him in the lobby of a hotel being used by several witnesses. When she looked into Pretus’s eyes, Stadler later told investigators, she felt the blood rush from her face. She knew immediately who he was.

She reported him to Naval authorities, but the accusation against Pretus was discussed only during a private session that was closed to the jury and was withheld from the proceeding’s transcript. NCIS launched an investigation, which was obtained by The Post. Authorities interviewed Stadler, inspected his service record and unsuccessfully attempted to retrieve video footage from the District hotel where Stadler said she saw him.

The investigation ended, however, when agents confronted Pretus. He refused to cooperate, according to military records, and invoked his right to remain silent.

Not until Thompson’s administrative hearing did the government try to use Pretus’s alleged involvement with Stadler, who was later kicked out of the Navy for lying about her relationship with an enlisted sailor. Known as a board of inquiry, three Marine officers voted 2 to 1 that Thompson should not have been found guilty of sexual misconduct. All three agreed that he should be allowed to stay in the service.

Pretus didn’t testify at that hearing, but much of what he told jurors at the trial focused on an incident alleged to have occurred just a few days after he had come to Annapolis.

On the night of April 30, 2011, Stadler and a female friend — both of whom knew Thompson through the school’s rifle team — attended the boozy annual croquet match between the academy and St. John’s College. Afterward, they stopped by Thompson’s house, just two blocks off campus.

The women claimed that Thompson served them shots of tequila before they played strip poker and staggered to his bedroom, where he had sex with both of them. Stadler said the sex was consensual and part of an ongoing relationship, but her friend later told authorities that she was too drunk to give him consent and alleged that he’d raped her. (The Post generally does not identify alleged victims of sexual assault.)

Pretus’s testimony was essential to rebutting their version of events.

He told the court that after returning from Annapolis to his home in North Carolina, he and his then-wife had gotten into an intense fight. Pretus said that the episode prompted him to talk by phone with Thompson several times on the same night the women later alleged that he had sex with them.

On the stand, Pretus was asked whether during their conversations, Thompson had talked about a pair of students coming to his home.

“He had mentioned that two female midshipmen — midshipmen from the rifle team — had stopped by his house inebriated and used the bathroom and left,” Pretus said, noting that Thompson had referred to them during a call at 8:12 p.m.

That statement was important for two reasons: It corroborated the story that Thompson has long insisted is the real truth, and it established a timeline that helped his defense team argue that the women had not stayed at his house as long as they’d alleged.

Pretus was then asked in court how he felt about Thompson allowing the women in his home.

“I was taken aback a little bit,” he said. “I’m sure I said something along the lines like ‘Wow, that’s not a good idea.’ ”

Pretus went on to testify that he had attended an academy event with Thompson in late 2011. There, he said, they ran into Stadler’s friend.

She testified that it was the first time that she’d seen Thompson since the alleged rape, saying that she felt “very awkward” during the conversation. A friend who was with her at the time told jurors she turned “bright red” and “wasn’t as outgoing as she normally is.”

But Pretus gave a different account of the meeting, asserting that the woman was “very girlish,” “very bubbly” and “not at all” awkward during the encounter.

Thompson, Pretus said in court, mentioned her again later that night.

“That’s one of those midshipmen that came over to my house that time. Do you remember when I told you that last spring?” Pretus testified that Thompson said to him.

“Oh, yeah,” Pretus told jurors he responded.

The two men remained close in the years following the trial, continuing to talk after Thompson served two months in a military prison and throughout his effort to clear his name. Pretus, meanwhile, remarried.

On the day the administrative board ruled in Thompson’s favor — just months before Pretus began teaching at the academy — the two men texted each other.

“Retained!!!” Thompson wrote, according to an exchange he later provided to The Post.

“F--- yeah,” Pretus responded, adding 21 exclamation points.

He kept texting: “Cigar time.” “Congrats.” “Call me when you can.”

Then another: “The nightmare is over!”

Thompson responded with a smiley face and, the next day, texted his friend once more.

“I beat them.”

Jennifer Jenkins contributed to this story.