The superintendent of the Virginia Military Institute resigned Monday morning, after Black cadets described relentless racism at the nation’s oldest state-supported military college and Gov. Ralph Northam ordered an independent probe of the school’s culture.

Retired Gen. J.H. Binford Peay III, 80, had been superintendent of the 181-year-old school since 2003.

In his resignation letter to John Boland, president of VMI’s Board of Visitors, Peay said that he’d been told by the governor’s chief of staff that Northam (D) and other state legislators had “lost confidence in my leadership” and “desired my resignation.”

“It has been the honor of my life to be the Superintendent of VMI for over seventeen years,” the retired four-star general wrote. “I always have and always will love the Institute, all of our cadets, alumni and the entire VMI family.”

During Peay’s tenure, multiple accounts of racist incidents have surfaced at VMI.

This month, The Washington Post documented how one Black student filed a complaint against a White adjunct professor who reminisced about her father’s Ku Klux Klan membership last year in the middle of class. In 2018, a White sophomore who told a Black freshman during Hell Week he would “lynch” his body and use his “dead corpse as a punching bag” was suspended, not expelled.

After The Post’s story was published, Northam, a 1981 VMI graduate, ordered an independent investigation into the Lexington school, which received $19 million in state funds in fiscal 2020. In a letter announcing the inquiry, Northam and other state officials said they had “deep concerns about the clear and appalling culture of ongoing structural racism” at VMI.

Boland rejected that description in a reply to the governor, saying that “systemic racism does not exist here and a fair and independent review will find that to be true.”

Peay emailed the VMI community last week, saying he did not believe systemic racism is present at the school.

VMI was the last public college in Virginia to integrate, admitting five Black students in 1968. It took a 1996 Supreme Court decision — written by Justice Ruth Bader Ginsburg — to end its resistance to allowing women to attend.

In announcing Peay’s resignation Monday, Boland said that he accepted it with “deep regret.” He said Peay was a “great American, patriot, and hero. He has profoundly changed our school for the better in all respects.”

According to the school’s website, Brig. Gen. Robert “Bob” Moreschi, deputy superintendent for academics and dean of faculty, will serve as acting superintendent. Moreschi began teaching at VMI in 2002 and became a tenured professor in 2008.

Peay did not return a message left at his home.

In a statement, Northam spokeswoman Alena Yarmosky said that “change is overdue at VMI, and the Board of Visitors bears a deep responsibility to embrace it.” She added: “Diversity is a fundamental commitment. Without this recognition, VMI cannot properly educate future citizen-soldiers nor live up to its values of honor, character and service.”

About 8 percent of VMI’s 1,700 students are Black. Many are athletes who said they weren’t fully aware of the school’s history or racial climate when they accepted scholarships.

The school, whose cadets fought and died for the slaveholding South during the Civil War, has long venerated its Confederate past. But the college has come under increasing pressure from Black alumni and cadets to remove the campus’s statue of Confederate Gen. Stonewall Jackson, who taught at VMI and was an enslaver of six people.

In July, Peay defended the statue of Jackson, calling him “a military genius” and a “staunch Christian.”

In an interview, Virginia Lt. Gov. Justin Fairfax (D) said VMI’s future — and its state funding — depends on school leaders demonstrating a “capacity to change” and that anyone who is unwilling to critically examine the school’s veneration of the Confederacy should leave.

Asked whether Boland should resign, Fairfax, an African American who is running for governor, said, “Anyone, including the chair of the Board of Visitors, who does not have the capacity to change and who cannot dramatically address the systemic racism at VMI no longer needs to be in a position of authority.”

Boland’s dismissal of systemic racism at VMI was “not appropriate,” Fairfax said, and the school needs to “operate with transparency with an eye toward getting to the truth so we can change the culture of VMI.”

The lieutenant governor, the descendant of an enslaved man, also said the board needs to reflect Virginia’s diversity. Of VMI’s 17 board members, three are Black. All of the school’s top officials, including the VMI chief of staff, the faculty dean and the inspector general/Title IX coordinator, are White men.

But Del. Kirk Cox (R-Colonial Heights) said Peay did not deserve to be pushed out after years of service in the military and at VMI before an investigation is launched.

“I am deeply disappointed that General Peay was not afforded the respect he deserved by the Governor and the other elected officials who saw fit to demand his resignation only days after calling for an investigation of incidents alleged in the news media,” Cox said in a statement, referencing the blackface scandal that engulfed Northam after racist images surfaced from his 1984 medical school yearbook page. “The Governor, in particular, should understand the importance of withholding judgment until the facts are in and should treat others with the same grace he once sought for himself.”

Cox condemned “the dangerous precedent” he said was being set and warned against Virginia’s universities becoming “political footballs tossed about by politicians who apparently lack the judgment and discretion to respect proper process and wait for the facts.”

Peay, who was born in Richmond in 1940, graduated from VMI with a civil engineering degree in 1962, according to his biography, which has been removed from the school’s website. In college, he was quarterback of the football team.

In the Army, Peay served two tours in the Vietnam War. Later, he became a senior aide to the chairman of the Joint Chiefs of Staff, served as an executive to the Army’s Chief of Staff and then assumed command of the famed 101st Airborne Division, which he led during Operations Desert Shield and Desert Storm in the Persian Gulf.

By the early 1990s, then a general, he was appointed as the 24th vice chief of staff for the Army. His final role was commander in chief of the U.S. Central Command in Florida from 1993 to 1997, helping oversee military operations in 20 countries in Africa, the Middle East, the Persian Gulf and South Asia.

Peay was highly decorated: He was awarded the Silver Star and Purple Heart. He and his wife have two sons, both graduates of VMI. Peay’s father, J.H.N. Peay Jr., was a member of the Class of 1929.

Peay was the school’s 14th superintendent, replacing Lt. General Josiah Bunting III, who called the Supreme Court’s decision ordering the school to go co-ed a “savage disappointment.”

In 2005, less than two years into his tenure, the school was forced to investigate cadets who dressed up in costumes parodying Nazis, Africans and gay people. The school initially played down the incident, with Peay’s spokesman at the time saying: “When I look at the pictures, I don’t see anything mean-spirited. What I see are college kids who are trying to use humor, and they missed.”

One photo showed three students posing as Nazis and making a Nazi salute; another had a mustache resembling Adolf Hitler’s. VMI punished several cadets with essays, 50-minute penalty marches, and lectures on decorum and civility.

In 2014, Peay faced one of his biggest controversies when the Education Department’s civil rights office investigated whether the school’s handling of a sexual assault violated the anti-discrimination law known as Title IX.

VMI was one of several schools under the Education Department’s scrutiny, but the incident was especially serious: A woman alleged that when she was a cadet, she was sexually assaulted by a VMI administrator.

In a video, the woman, who was not named in the complaint, said that when she met with Peay in October 2011 in his office, he asked her: “Do you believe in your heart of hearts that you asked [the alleged assailant] to stop? Because I’m confused on how you let it progress as far as it did.”

“He didn’t ask me if a sexual assault happened. He knew that something happened,” she said. “He was asking me whether or not it was consensual. I’ll never forget the look of hate he had towards me.”

Laura Vozzella contributed to this report.