Marine Maj. Mark Thompson (left) faces new charges in a Naval Academy sexual misconduct case. Marine Maj. Michael Pretus (right) was removed from his teaching job after he acknowledged he’d had sex with a female midshipman before arriving to work in Annapolis. (Left: Nikki Kahn/TWP; Right: TWP/Left: Nikki Kahn/TWP; Right: TWP)

In the wake of a widening sexual misconduct scandal at the U.S. Naval Academy, military officials couldn’t explain how a Marine Corps officer had been assigned to teach at the school after he was investigated for having sex with a female midshipman.

It’s now clear, however, that Maj. Michael Pretus became an instructor not only because of a vast communication failure among military leaders, but also because of a systemic flaw in the way the Naval Academy vets dozens of its staffers, according to a Washington Post examination that also found significant errors in how the service academies and the Pentagon reports sexual assaults on students to Congress.

The military did vet Pretus when he was selected in 2012 to get an advanced degree in history that would prepare him to teach. But during the two years and eight months between when he got the news and when he was scheduled to start working in Annapolis, Pretus faced a crisis: A former midshipman told authorities that while attending the academy in 2011, she had a threesome with him and another Marine, Maj. Mark Thompson, a former history teacher later convicted of sexual misconduct. Her accusation against Pretus, now 40, triggered a criminal investigation that, according to military records, ended only after he refused to cooperate.

Despite the inquiry, he became an instructor in August 2014. Not until a Post story on Thompson’s case did academy leaders learn about the allegations against Pretus, who was removed from his position in April.

View of the main entrance gate of the U.S. Naval Academy in Annapolis in April. (Linda Davidson/The Washington Post)

Twenty-eight of the academy’s current faculty members, including 22 Marines, arrived on campus the same way Pretus and many others have since the advanced-degree program was launched in 2006, the school said. They were selected to get a master’s degree and then given two to three years to attend a college and move to Annapolis to work in the classroom. Though the military rigorously inspects their service records during the initial selection process, the academy acknowledged that they aren’t formally vetted again before they’re given positions of authority over midshipmen.

This means that, as in Pretus’s case, the academy may never learn about serious issues that could arise during the years while officers are earning their degrees.

In a statement, Cmdr. John Schofield, a Naval Academy spokesman, called the school’s failure to flag Pretus an “aberration, and not indicative of the normal and historical effectiveness of the system.”

But how does the academy know others like Pretus, who also served as a mentor to aspiring Marines, aren’t working with midshipmen right now?

“In short, we don’t,” Schofield said. “We believe the vetting process is effective. We work very hard to ensure the men and women of the Naval Academy Brigade of Midshipmen are educated and represented by only the very best faculty and staff.”

Sen. Kirsten Gillibrand (D-N.Y.), a longtime critic of how the military deals with sexual assault, called the academy’s defense of its vetting process “another example of an unwillingness to change the status quo.”

Sen. Claire McCaskill (D-Mo.), a former prosecutor who has worked for years to reform the military justice system, was equally critical.

“Americans rightfully expect that we should have in place the highest possible standards for vetting the instructors at those academies, and anything short of that is unacceptable,” she told The Post. “I expect the Naval Academy’s leaders to take that responsibility seriously and immediately get to work to close any loopholes in their vetting process.”

The pervasiveness of sexual assault among cadets and midshipmen at the Naval Academy, the U.S. Military Academy at West Point and the Air Force Academy — training grounds for the country’s military leaders — has come under intense scrutiny in recent years. But what has received far less public attention is the potential threat of misbehavior posed by staff.

In the past decade, at least 14 people who worked for or at the service academies were punished for committing acts of sexual misconduct against students or engaging in inappropriate relationships with them, according to military records and information provided by the three schools.

Among the cases from the past three years: A lieutenant commander who taught at the Naval Academy was expelled from the service after he fondled a female midshipman. A captain at the Air Force Academy was pulled from his position in the athletic department after he made sexual advances toward female cadets. A sergeant at West Point was sentenced to 33 months in prison after he secretly filmed female cadets in the campus’s showers and bathrooms.

At the Naval Academy, which has had the most incidents since 2006, it’s difficult to determine exactly how often employees victimize students. The military is required by Congress to produce annual accounts detailing sexual harassment and violence at all three schools, but The Post discovered serious inaccuracies in the reported Naval Academy cases that call into question the records’ reliability.

Since at least 2007, each report has included a summary of sexual assault allegations from the previous school year. But none of them mentioned Thompson, whose case was triggered in 2012 when a student accused him of rape.

In addition to that omission, the summary covering the 2014-2015 school year stated that a commander at the Naval Academy grabbed a midshipman by the hips and tried to “put his tongue in Victim’s mouth.” Though the record indicated that he received what the military calls “non-judicial punishment,” academy officials now insist the man wasn’t a Naval officer — as the report states — but a civilian. According to a school staff member with direct knowledge of the situation, the offender coached a women’s club sports team.

One case in the 2013-2014 summary was erroneously included in the next annual report as well, the academy acknowledged. Another year, Navy midshipmen were repeatedly referred to as “cadets,” a glaring mistake within the military community.

McCaskill’s office described the missteps as “troubling,” and Gillibrand argued that they further expose the military’s inability or unwillingness to appropriately address sexual misconduct within its ranks.

“The document problem is a symptom of a larger issue that they just don’t take these cases seriously,” she said. “They continue to say ‘We got this, we can handle this.’ . . . The evidence doesn’t bear that out.”

Academy and Pentagon officials blamed the blunders on human error. Air Force Col. J.R. Twiford, chief of staff at the Pentagon’s sexual assault prevention and response office, stressed that the military does take the issue seriously, pointing to an automated database that was created in 2014 to track such cases in a more organized way. He also noted that “none of these errors impact the victim or the justice outcome for the accused.”

The Naval Academy, Schofield said, intends to do whatever it can to ensure that any reporting problems are addressed and don’t continue.

Teachers at almost all U.S. universities who sleep with students could face serious consequences, but for service members at academies, it’s a crime — even if the sex is consensual.

Although Pretus’s case has brought more unflattering attention to the academy, he is not counted among the staff members who have engaged in sexual misconduct with students.

What led to his removal from campus began with an April 2011 trip to Annapolis, where he delivered a guest lecture to Thompson’s history class. Pretus spoke to students about his harrowing combat experience in Iraq.

Afterward, according to investigators, the longtime friends went to Thompson’s home and both had sex with a midshipman named Sarah Stadler. Back then, she and Thompson were in an illicit relationship prohibited by military law.

Days later, Stadler and a 21-year-old female classmate walked to Thompson’s house after a long day of drinking. 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. Stadler’s friend later alleged to authorities that he’d raped her because she was too drunk to give consent.

Around the time of her accusation, Pretus announced on Facebook that he’d been chosen to get a master’s degree and eventually teach at the academy.

“This is a dream come true!” he wrote on Jan. 20, 2012, referring to himself as “the luckiest guy in the world.”

At Thompson’s trial in 2013, Pretus provided key testimony that rebutted the women’s version of events. He asserted that in a call on the night of the alleged assault, Thompson told him two female midshipmen had stopped by to the use the bathroom and left.

But during the court-martial, Stadler spotted Pretus and told military investigators that, though she couldn’t recall his name, she knew he was the Marine who’d joined in the tryst with her and Thompson.

The Naval Criminal Investigative Service interviewed Stadler and inspected Pretus’s service record, but their inquiry ended when he invoked his right to remain silent.

Academy officials probably would have never learned about the accusation had Thompson not fought so hard to clear his own name. At trial, he was acquitted of the rape but convicted of five other charges related to sexual misconduct. Thompson later brought his story to The Post, which discovered that he had lied under oath to an administrative board in 2014. In April, the Marines charged him with three additional crimes. Pretus, who did not respond to requests for comment on this story, has agreed to testify against Thompson in the new case and has acknowledged to prosecutors that both men had sex with Stadler.

Two months ago, Schofield, the academy spokesman, said that “under no circumstances” would Pretus have been allowed to teach there had the school known about his past. But officials in the Marine Corps, the Judge Advocate General of the Navy, NCIS and Pretus’s former command in New Orleans all knew about the allegation and didn’t inform the school.

Still, the academy confirmed that it is ultimately accountable for the people who work there. And, over the past decade, no fewer than a half-dozen of those people have been accused of acting inappropriately toward students.

In 2007, Navy Lt. Cmdr. John Thomas Matthew Lee, a Catholic priest, pleaded guilty to forcible sodomy, aggravated assault and other crimes committed against three servicemen, including a 20-year-old midshipman.

That same year, Navy Cmdr. Kevin J. Ronan, a doctor, was sentenced to nearly four years in prison after he secretly recorded “sex tapes” of nine midshipmen he allowed to stay at his home through a sponsorship program. Although Ronan was not on academy staff, he often treated students.

During the 2012-2013 school year, a foreign-language teacher from China was accused of sexual assault after she spanked a student who had incorrectly answered her questions, according to military records. The woman no longer teaches in Annapolis.

The Air Force Academy said that five of its staff members have been removed from their positions in the past 10 years for inappropriate behavior with students, including a female captain in 2014 and a female master sergeant in 2013 who each had sexual relationships with male cadets.

The Air Force Academy does not have an advanced-degree program comparable to that of the Naval Academy, but West Point does — and its version is much more robust.

Thousands of Army officers have joined the school’s staff that way, including more than 300 working there now. West Point also doesn’t re-scrutinize service members after they earn their degrees, but a school spokesman said he knew of no cases like Pretus’s.

In May, after The Post asked all three academies how many staff members had been ousted from their positions because of sexual misconduct with students, West Point offered just one from the past decade: Michael McClendon, the sergeant who in 2014 was sent to prison for secretly recording cadets.

But a month later, public affairs specialist Francis J. DeMaro Jr. provided a second case.

Last year, he said in an email, an Army captain lost her job after “sexual contact while intoxicated against two male cadets at a football game in late fall 2015.”

And why was that case not included in West Point’s original response?

“I am told,” DeMaro responded, “it was an oversight.”

Jennifer Jenkins contributed to this report.