Marine Maj. Mark Thompson at the U.S. Naval Academy, where two female students accused the former history teacher of having sex with them. (Nikki Kahn/The Washington Post)

The military has launched a new investigation of Marine Maj. Mark Thompson, the former U.S. Naval Academy instructor who insisted that he was innocent of sexual misconduct with two young women while they were students at the school.

Following Washington Post revelations about Thompson, a Marine Corps prosecutor and an investigator met this week with one of his accusers, Sarah Stadler, to review the contents of her long-missing cellphone, she said.

“I can confirm that the Marine Corps is examining new evidence that has recently come to light as a result of the Washington Post article about Maj. Thompson’s case,” Rex A. Runyon, a Marine Corps spokesman, said in an email. “I cannot provide additional details as it is our policy not to discuss ongoing investigations.”

Before the meeting, Stadler said she sent the prosecutor several images of text conversations between her and Thompson, who was convicted in 2013 of five counts of sexual misconduct but was allowed to remain a Marine.

A number of the more than 650 messages she and Thompson exchanged appear to contradict what he said under oath in 2014 to an administrative board deciding whether he should be expelled from the armed forces. Military law experts say that such wrongdoing can lead to serious consequences. Service members who make a false official statement may face up to five years’ confinement and a dishonorable discharge.

Sarah Stadler holds her long missing cell phone, showing a text conversation with Maj. Mark Thompson. Its discovery has launched a new investigation into Thompson by the military. (Phelan M. Ebenhack/For The Washington Post)

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

In response to an email from The Post, Thompson asked for more information but didn’t answer a request for comment on the government’s actions. His attorneys also did not respond to requests for comment.

Stadler first heard from the prosecutor last week, she said. When he asked what she hoped would happen to Thompson, Stadler told him that she wanted the former history instructor court-martialed and kicked out of the military.

The prosecutor, she said, told her that Thompson could go to trial a second time, although the military could also pursue administrative punishment.

“I hope he gets dismissed from the Marine Corps,” she said, “before he has a chance to retire.”

Thompson and military officials have said that he will be eligible for retirement in November.

The Marine major has been fighting to prove his innocence since Stadler and a 21-year-old woman alleged that he had sex with them amid a drunken night of strip poker at his Annapolis home. Stadler said the 2011 liaison was consensual and part of an ongoing relationship. Her friend called it rape.

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)

At his court-martial in 2013, Thompson was acquitted of the assault charge, but the jury still concluded that he’d had an inappropriate sexual relationship with the women, whom he knew through the school’s rifle team. He was found guilty of five lesser offenses and sentenced to two months in a military brig and fined $60,000.

In 2014, his case was reviewed again at what is known as a board of inquiry hearing. There, three Marine officers were assigned to decide whether Thompson should be discharged for his crimes.

The combat veteran testified that he was never friends with Stadler outside the rifle team, insisting that his interactions with her were appropriate, professional and within academy guidelines.

[Why sex assault reports have spiked at the Naval Academy, West Point and Air Force Academy]

He told the board that she had created “a complete fiction about a relationship that never existed” — and specifically denied ever having any sexual conversations with her. The board members believed him, allowing him to remain a Marine and even publicly decrying his convictions as unjust.

But many text messages on Stadler’s old phone — which she discovered after being contacted by The Post — strongly imply that the two were involved in an inappropriate relationship. One exchange was sexually explicit.

The texts also revealed that Thompson had misrepresented to the board the last time he saw Stadler. Stadler had alleged during his court-martial that they had sex a final time on the night of her May 2011 graduation, a time when Thompson had a compelling alibi. The texts, however, show that the two actually saw each other at 11:30 p.m. the following night.

At his board hearing, Thompson testified that the last time he remembered seeing Stadler was nearly one month earlier.

When confronted by The Post in January this year, Thompson acknowledged that Stadler had come to his house the night after graduation but insisted she did so only to give him a pair of commemorative glasses and her photograph. He still denied ever having sex with her.

Asked why he hadn’t been honest with authorities about the rendezvous, Thompson described the immense pressure the rape charge had placed on him.

“I simply had to, when they were coming after me for 41 years,” Thompson said. “I can’t begin to say, you know, how terrifying that is.”

What will happen to him next could take months to determine.

Meanwhile, Stadler is contending with her own challenges. She was expelled from the military in 2014 after initially lying about her relationship with an enlisted sailor in California. The government has since tried to recoup more than $85,000 for the time she owed the Navy after graduating from the academy.

Stadler wants that debt forgiven, and she recently discussed her options with military attorneys, both active-duty and retired. She had hoped that the evidence contained on her phone might help her cause, but she said that even without assurances that her debt will ever be erased, she is eager to cooperate with investigators.

“The right thing to do,” she said, “is to see that justice is served.”