Ms. Flournoy’s résumé had seemed potentially right for the moment. She served in the Pentagon first under President Bill Clinton, and from 2009 to 2012 she was the under secretary of defense for policy in the Obama administration — the highest-ranking role for a woman in the Pentagon at the time. She removed her name from contention for the top job in 2014, when Mr. Obama initially was considering her to succeed Defense Secretary Chuck Hagel.

She instead became a senior adviser at the Boston Consulting Group, then went on to help found WestExec Advisors, a consulting firm. Her second shot at the job was scuttled when Hillary Clinton — who was widely expected to name her — lost the presidential election in 2016.

Ms. Flournoy was known for seamlessly moving between the civilian and active-duty sides of the Pentagon, bridging the often impenetrable gap between those in uniform and those in suits — a skill that some fear may be lost with a retired general in the role. She did so, her fans said, by translating the political imperatives of civilians to the active-duty military world and carefully helping the civilian side understand the military’s practical needs and limitations in seeing through the policy goals of elected officials.

“She is enormously talented, and the last thing I think about is that she is a woman,” said Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff at the time of the Afghanistan surge, which she helped advocate to the Obama White House. “From my perspective that is a great thing.”

Yet among women who toil in the national security trenches, an area where men — and what Ms. Flournoy often refers to as their “mini-mes” who succeed them — have historically dominated, Ms. Flournoy is widely regarded as an essential mentor.

“An entire generation of national security women used her as their role model in how to navigate a male-dominated job,” said Representative Elissa Slotkin, Democrat of Michigan, who also worked for Ms. Flournoy. “The lesson she provided for women is that you have to always be the best prepared in the room. I literally learned that from her, and I now pass that down to the young women who work for me.”

Celeste Wallander, the president of the U.S.-Russia Foundation, is among scores of women who consider Ms. Flournoy central to their successful careers. Ms. Wallander recalled a time in 1989 when the two were both academics at Harvard, where Ms. Wallander, very junior, was usually left off the invitation list for dinners and other events with major players in her field. Ms. Flournoy quietly had her added to the lists. “I got to meet people because I was at the table now,” Ms. Wallander said.

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