Air Force Academy Superintendent Lt. Gen. Michelle Johnson, left, and football team members, listens as President Donald Trump speaks in the Rose Garden of the White House in Washington during a presentation ceremony of the Commander-in-Chief trophy to the Air Force Academy football team. (AP Photo/Susan Walsh)

The head of the U.S. Air Force Academy is stepping down after four years on the job.

When Lieutenant General Michelle Johnson first took the helm, the Air Force Academy had removed four of its top officials following the systematic cover-up of rape at the school. Johnson, the first woman to lead the academy, pledged to address sexual assault and harassment.

Johnson recently visited Harvard's Kennedy School of Government to discuss values and ethics in the military. WGBH’s Kirk Carapezza sat down with her in Cambridge. In a wide-ranging interview, they talked about her crusade against sexual assault in the military and what the Trump administration means for victims’ rights.

Growing up in a small town in Iowa, Johnson says she didn’t realize that President Gerald Ford had signed legislation directing the military service academies to admit women.

"I just knew that after talking to a liaison, it was this great education,” Johnson said. “I was a basketball player, and I could serve my country for a while. And that was 40 years ago and then I'm still here.”

Johnson was part of the Academy's second co-ed class. She went on to serve as the first-ever female presidential aide responsible for carrying the so-called nuclear football.

In 2013, appointed by President Barack Obama, Johnson was put in charge of the Air Force Academy.

She says there was some backlash when older alumni showed up on campus and expected to see a man at the top.

“They were trying to sort that out,” she said, looking back. “The hate mail quit about six months in.”

Johnson took it all in stride. Since then, she’s been responsible for more than 16,000 cadets, a quarter of whom are women.

Because Johnson was one of the Academy’s first female cadets, she says she understands what it’s like to be a woman at an institution dominated by men and plagued by sexual harassment.

“In those early years, there was more this reaction to change, and it was really in our face,” Johnson said. “‘Why are you here?’ ‘Are you lowering standards?’”

Johnson says the harassment was “aggressive,” but she overcame it. She learned to fly, logging more than 3,600 hours as a command pilot.

As the head of the Air Force Academy, she’s taken on a different challenge: sexual assault in the military. She has spoken much more candidly about the issue than her predecessors ever did, hosted seminars on prevention for other higher education institutions and provided additional support for victims.

“In a way, military commanders have an advantage in that we have law enforcement arms so we automatically have due process for subjects as well as for victims,” Johnson said. “Not all colleges are resourced that way, so for us there are higher expectations. We're the stewards of government resources and answer to the American people so we really have to get to this right."

Listen to Kirk Carapezza’s extended interview with Lieutenant General Johnson:

A recent Department of Defense survey found the number of Air Force cadets experiencing unwanted sexual contact increased from 126 in 2014 to 150 in 2016. Johnson says an increase in reports proves that victims trust the Academy will handle their cases fairly.

Many studies have found that about 20 percent of women are sexually assaulted in college, but analysis by the American Association of University Women finds the vast majority of colleges didn't report a single rape on campus in 2015.

Under the Obama administration, the Office of Civil Rights had urged the Academy as well as other colleges and universities to adopt a lower burden of proof in sexual assault cases. Now, conservatives are pressuring the Trump administration to rescind that guidance.

During the 2016 presidential campaign, a tape surfaced of then-candidate Donald Trump talking about his ability to grab women’s genitalia. Many victims' rights advocates saw his eventual election as a setback, but Johnson doesn't necessarily see it that way.

"The discussion about sexual assault prevention is vibrant,” she said. “All of our cadets come from somewhere. They come from every congressional district in the country. And some come from Ferguson. Some come from places where there have been natural disasters. Some are of Jewish faith, and they see hate crimes in cemeteries. So more and more we need to talk about these things and have dialogue."

At a time when many Americans have lost faith in their institutions, Johnson is optimistic. Of course, as an apolitical military leader, that's part of her job. She says morale among cadets remains high.

"The whole of government are a lot of people and what's beautiful is our oath of office is to the Constitution,” Johnson said. “We don't have a person that you take the oath to. It's to the Constitution."

Shortly after our interview with Lieutenant General Johnson, she announced her retirement.

The Air Force Academy says she had long planned to hang up her uniform, and it hasn't announced who will replace her.

WGBH's Tristan Cimini contributed to this report.