The Navy’s top leadership believed that Rear Adm. Stephen D. Barnett was by far the best choice to lead the command that oversees the Navy’s bases at home and abroad.

He had more experience than the other candidates and had successfully managed the aftermath of one of the Navy’s biggest messes, a fuel spill that contaminated an aquifer on a base in Hawaii, sickening thousands.

The final decision this spring fell to Defense Secretary Pete Hegseth.

To many in the Navy, Admiral Barnett’s promotion seemed like a foregone conclusion.

The officer, however, had a big strike against him. Like other Black military leaders, he had been encouraged by his superiors to help the Navy recruit and retain minority officers, who remain significantly underrepresented in the force. His years-old remarks on the importance of diversity had been flagged in a secret vetting process designed to weed out senior leaders whom Mr. Hegseth and his team pegged as a problem.

Instead of Admiral Barnett, Mr. Hegseth selected a white officer who was the Navy leadership’s third choice.

So far this year, Mr. Hegseth has blocked the promotions of at least 40 senior officers to general and admiral ranks. About half of those are women or members of minority groups.

This article, based on interviews with 15 current and former military and administration officials, is a look inside the process Mr. Hegseth and his team have used to halt the advancement of senior officers for reasons that have nothing to do with fighting wars or job performance.

It tells the story of one Black officer — Admiral Barnett — whose blocked promotion shocked and angered senior Navy officials.

The officials discussed sensitive personnel matters on the condition of anonymity. Admiral Barnett, who is expected to retire, declined a request for comment. A Pentagon spokesman did not respond to a detailed list of questions.

In books and speeches, Mr. Hegseth has maintained that the Pentagon’s push over the past decade to build a more diverse force had elevated women and minority officers to senior jobs that they had not earned.

“When I think about my career in uniform, in almost every instance where there has been poor leadership or people in positions they’re not qualified for, it was based on either the reality or the perception of a ‘diversity hire,’” Mr. Hegseth, a former major in the Army National Guard, wrote in his 2024 book “The War on Warriors.”

As defense secretary, he has promised to install a new promotion system that will be “ruthlessly meritocratic” and “focused squarely” on “warfighting ability.”

In practice, though, his approach has made it harder for Black and female officers to get promoted to senior ranks, even when their records are exemplary.

Such was the case with Admiral Barnett. In 2021, he was invited to speak at a Black History Month event at a naval base in Maryland.

He talked about his career as a flight officer on Navy P-3 Orions, which track enemy submarines. “Just one generation before me, it was nearly unthinkable for a Black person to become a naval aviator,” he said.

He reflected on his mentors, downplaying the importance of race. “What helped me was people who didn’t look like me,” he said.

And he spoke about building a force that better represented the nation it serves.

“As the country becomes more diverse, it makes sense for our military to become more diverse,” Admiral Barnett said. “Monolithic organizations cannot and will not survive.”

At the time, the country was wrestling with the aftermath of the death of George Floyd, an unarmed Black man who was murdered by a white Minneapolis police officer nine months earlier. The Navy had just released a 142-page report with recommendations to remove barriers that had held back high-performing women and minority sailors.

Five years later, Mr. Hegseth was leading the Pentagon. Now Admiral Barnett’s remarks were being cited as a reason to deny him a promotion that senior Navy officials said he deserved.

‘It’s Black over white’

Mr. Hegseth has argued that the troops most likely to suffer discrimination in the military are white.

He traced the problem to the protests and racial reckoning that followed Mr. Floyd’s murder. The Pentagon’s generals and admirals, he wrote in his 2024 book, started searching for evidence of institutional bias that did not exist. In the process, he argued, they destroyed the military’s meritocratic culture.

“It’s Black over white. Female over male. Gay over straight,” Mr. Hegseth wrote.

Internal Pentagon studies told a different story. Nearly a third of Black U.S. military troops reported experiencing racial discrimination, harassment or both during a 12-month period, according to a survey conducted during President Trump’s first term.

In his book, Mr. Hegseth dismissed such data.

As secretary of defense, he has fired or sidelined more than two dozen generals and admirals. Among those dismissed were Gen. Charles Q. Brown Jr., the second Black man to serve as chairman of the Joint Chiefs of Staff, and Adm. Lisa Franchetti, the first woman to lead the Navy.

Those ousters were all publicly announced. The extent of Mr. Hegseth’s vetoing of generals and admirals selected for promotion has remained secret until now.

By law, one-star and two-star officers are chosen by promotion selection boards made up of senior military officers. The meetings are so confidential that board members are not permitted to tell others that they are part of the process.

Last year, Mr. Hegseth and his top aides ordered the Army, Navy, Air Force and Marine Corps to do online searches of the officers selected by the boards, to look for photos, videos or news articles that might draw Mr. Hegseth’s ire, current and former defense officials said.

The officials undertaking the reviews hoped that if they could show that the officers had been following previous Pentagon policies that Mr. Hegseth would allow their nominations to go forward to the White House and Congress for final approval.

Inside the Pentagon, such material was referred to as “D-ROG,” short for derogatory material.

Once the reviews led by each military service were complete, Mr. Hegseth’s staff conducted their own searches to make sure that the services had not missed or intentionally ignored anything.

It was not clear whether Mr. Hegseth had the authority to pull names off the list. Congress had entrusted management of one-star and two-star promotion boards to the service secretaries, not the secretary of defense.

The first test case was with an Army one-star promotion board. Last fall, Mr. Hegseth ordered Army Secretary Daniel P. Driscoll to remove two Black and two female officers from a 29-person promotion list. Mr. Driscoll, citing their decades-long records of exemplary service, repeatedly refused. The standoff lasted months.

Finally, in March, Mr. Hegseth removed the officers’ names from the list and forwarded it to the White House.

Around the same time, a senior aide to Mr. Hegseth accused the Navy, in a handwritten note, of promoting candidates that the defense secretary believed should have been blocked.

Mr. Hegseth’s aides wanted the Navy to form a new promotion board that would choose a new list, Navy officials said.

The Navy pushed back. Mr. Hegseth instead removed nine officers from the Navy’s original 31-person list.

Soon Mr. Hegseth was pulling officers from nearly every active duty and reserve officer promotion list. Officers who had spoken publicly about the importance of diversity in the ranks were removed from lists. So too were those who had strongly urged their troops to get the Covid vaccine.

Mr. Hegseth has removed a total of 32 officers from Air Force and Navy one-star and two-star promotion lists, defense officials said. The only Black officer and the only female officer were removed from a Marine Corps promotion list. The two Marines’ promotions are in limbo.

Much of the vetting process has remained shrouded in secrecy. In some instances, officers up for promotions were not told that they had been removed from the lists. Mr. Hegseth also has refused to give Congress the names of officers pulled from the lists, officials said. The Senate’s version of the 2027 defense bill would require Mr. Hegseth to provide “a written justification and notification” when removing an officer from a promotion list.

Even the services often are not told why individual officers are vetoed.

Military officials, though, said they have noticed patterns. Officers who had commanded aircraft carriers or amphibious assault ships have been especially vulnerable. The reason: Those ships have public affairs sailors on board who documented their skippers participating in events related to diversity or the Covid vaccine.

Now those articles, videos and photos, posted on the Navy websites, were being used against them, current and former Navy officials said.

Among those targeted was Vice Adm. Sara Joyner, a three-star fighter pilot who military officials wanted to move to a higher-profile job in the Pentagon.

Admiral Joyner had spoken at events designed to encourage and mentor female aviators and submariners. She also had appeared in a Navy recruiting ad describing her childhood and her trailblazing career as the first woman to command a carrier air wing.

“One day, everyone will see that I’m not just a girl with a dream,” her character in the 2021 ad said. “I’m a sailor with one.”

To Mr. Hegseth, the appearances and the ad were a big problem.

Unlike with the one- and two-star ranks, there are no promotion boards for most three-star and four-star generals and admirals. Typically, the service secretaries and service chiefs identify their preferred candidate among two or three choices and present them to the chairman of the Joint Chiefs of Staff, who can weigh in. Then the candidates are sent to the defense secretary, who picks a nominee from the shortlist.

Admiral Joyner worked for Gen. Dan Caine, the chairman of the Joint Chiefs of Staff, running a team that conducted classified war games and assessments of new weapon systems. General Caine urged Mr. Hegseth to nominate her for the new position, current and former officials said. He also asked John Phelan, then the Navy secretary, to help persuade Mr. Hegseth to reconsider her promotion.

Their interventions failed. Senior officers who are not promoted are usually expected to leave. The Times was unable to reach Admiral Joyner for comment. She retired last fall.

A high-flying Navy career

When Admiral Barnett joined the Navy in 1991, he never expected he would become an admiral. He didn’t come from a family with a deep history of military service and had not attended the U.S. Naval Academy.

In 2023, he shared the story of his life and career in an interview with his hometown radio station in Columbia, Tenn.

Admiral Barnett’s interest in the Navy was piqued by one of his fraternity brothers at Tennessee State University, a historically Black college. At the time, he was married with a child. The Navy offered a good salary, adventure, health care and stability.

“So, one day after thermodynamics class, I joined,” he told the radio host. “I kind of did it on a whim.”

Admiral Barnett, who went by the call sign “Big Daddy,” recalled how much he enjoyed being part of a team. His P-3 surveillance plane had a crew of 11 sailors who flew sorties lasting as long as 10 hours. He rose through the ranks flying more than 250 missions in Iraq and serving in increasingly sensitive commands.

Then, in 2021, the Navy’s Red Hill Bulk Fuel Facility leaked petroleum into an aquifer in Hawaii that tens of thousands of residents depended on for their drinking water.

Adm. Samuel Paparo, who was serving as commander of the U.S. Pacific Fleet, asked Admiral Barnett to rush to Joint Base Pearl Harbor-Hickam in Hawaii to lead the cleanup.

“I only need you there for 12 months,” he recalled Admiral Paparo telling him. Admiral Barnett remained for more than three years, working to decontaminate the aquifer and win back the trust of scared and angry residents.

In a statement, Senator Mazie Hirono, Democrat of Hawaii, recalled him as “an important and trusted partner.”

“He was proactive, communicative and professional,” she said.

Admiral Barnett’s work fixing Red Hill and experience overseeing three large regional commands made him the Navy’s top pick for a third star and the job running its bases.

Before senior Navy officials recommended Admiral Barnett for the promotion, they searched the internet for anything in his public record that might offend Mr. Hegseth. Navy officials hoped that, if they put Admiral Barnett’s remarks in context, Mr. Hegseth might overlook them.

Admiral Barnett had spoken at a few Black History month events and talked in interviews about the legacy of service members, like Doris “Dorie” Miller, who became the first Black recipient of the Navy Cross for his heroics at Pearl Harbor. A photo of Mr. Miller hung in Admiral Barnett’s Hawaii office.

In 2018, Admiral Barnett had appeared at Navy-sponsored event during L.G.B.T.Q. Pride month. “Together, we can make the world safer, freer and more equal for everyone,” he said, according to an article posted on a Navy website.

His statements were in line with Pentagon policy at the time, the Navy concluded.

“If one were scrutinizing with extreme sensitivity, the only potential ‘signals’ are those of empathy and inclusivity,” according to an internal review obtained by The New York Times. “His digital footprint is remarkably disciplined and issue focused.”

Mr. Phelan, the Navy’s senior civilian leader, and Adm. Daryl Caudle, its highest-ranking officer, picked Admiral Barnett to lead Navy Installations Command. General Caine agreed.

The final decision, though, did not fall to the Navy or the chairman. It was made by Mr. Hegseth, who decided that Admiral Barnett should not advance.

Julie Tate contributed research.