Marine Major. Mark Thompson is photographed at the U.S. Naval Academy, where he taught history. He faces new criminal charges in a sexual misconduct case. (Nikki Kahn/The Washington Post)

The military has filed new criminal charges against Marine Maj. Mark Thompson, a former U.S. Naval Academy instructor who insisted that he had been unfairly convicted of sexual misconduct with two female midshipmen.

After revelations about his case in The Washington Post, the military has now charged Thompson with making a false official statement and conduct unbecoming an officer and a gentleman.

If convicted of lying under oath, Thompson could face up to five years in prison, a dismissal from the service and a total loss of his retirement benefits. Retired U.S. Air Force judge advocate Rachel VanLandingham said the potential penalty for the conduct-unbecoming accusation depends on the underlying offense.

The Marine Corps will hold an Article 32 preliminary hearing in May in Quantico, Va., to determine whether the case should proceed to a court-martial.

Thompson, who served in Afghanistan, has long fought to prove he was falsely accused of having sex with two students in 2011, but a Post investigation revealed that he’d been dishonest when he testified under oath in 2014 to an administrative board deciding whether he should be expelled from the Corps. Asked in January of this year why he had lied to authorities, Thompson described the immense pressure he faced after one of the women asserted that he’d raped her.

“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.”

Thompson, whose defense attorney declined to comment, was acquitted of the rape charge but found guilty of five lesser offenses. He served two months in a military brig and was fined $60,000.

After the Post story was published last month, the Marine Corps launched a new investigation, rapidly building a case against the 19-year veteran.

A prosecutor met earlier this month with one of the accusers, Sarah Stadler, to review the contents of her long-missing cellphone. A number of the more than 650 messages she and Thompson exchanged appear to contradict several assertions he made at the administrative hearing. Then, earlier this week, Marine Maj. Michael Pretus — a key witness for Thompson’s defense at his 2013 court-martial — told The Post that he would now serve as a witness for the prosecution against his longtime friend.

Pretus was removed this week from his position as a Naval Academy instructor after school officials learned of his involvement in Thompson’s case. In 2013, Stadler had alleged that, while a student, she had a threesome with the men at Thompon’s house. Military records show that accusation led to a criminal investigation into Pretus, which ended after he refused to cooperate and invoked his right to remain silent.

“I feel vindicated,” Stadler said of the new charges. “I feel relieved that this might now finally be coming to an end and that the end might actually be justice.”

Thompson, however, has always maintained that he did nothing wrong.

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.

He claimed that they asked to use the bathroom, did so and left. The women claimed that he served them shots of tequila before they played strip poker and staggered to his bedroom, where he had sex with both of them. Under military law, a threesome is considered an indecent act — a serious crime.

Stadler — later dismissed from the Navy for lying about her relationship with an enlisted sailor after she’d graduated from the academy — said the sex was consensual and part of an ongoing relationship. But her friend told authorities that she was too drunk to give Thompson consent, alleging that he’d raped her.

In 2014, a year after his sexual misconduct convictions, Thompson’s 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.

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 Thompson, allowing him to remain a Marine and even decrying his convictions as unjust. Soon after, Thompson asked The Post to examine his case, arguing he was innocent.

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. She had alleged during his trial 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 in January of this year by The Post, 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.

VanLandingham, who teaches at Southwestern Law School, said Thompson had put himself in jeopardy.

“A military officer who, as an instructor at a premiere military academy, sleeps with his students commits a serious fraternization crime,” she said. “However, a military officer who lies under oath about it, plus arrogantly engages others to help spin his web of lies on the front page of the nation’s leading newspaper, is deserving of years in jail and our collective condemnation.”