Defense Secretary Pete Hegseth decided in early 2025 to spike Gen. Christopher T. Donahue's nomination to be the top U.S. military officer in Europe. Mr. Hegseth believed that President Trump wanted heads to roll for the deaths of 13 U.S. service members in a suicide bombing at the Kabul airport during the U.S. withdrawal from Afghanistan in 2021.

General Donahue was not responsible for security at the bombing site. But he was a top commander at the airport, and so Mr. Hegseth decided he needed to go. It fell to Joe Kasper, Mr. Hegseth’s chief of staff, to try to convince him that he was wrong. Mr. Kasper asked a senior Pentagon official to prepare a card with a half-dozen bullet points laying out the facts in General Donahue’s defense, current and former officials said.

He took it with him in March of last year as he and Mr. Hegseth sped through traffic to the White House for a press event. For those few minutes in the car, Mr. Kasper knew he would have his boss’s undivided attention. Sirens were blaring.

He handed Mr. Hegseth the card. These were the facts of General Donahue’s three-decade career: He had seen more combat in his 20-plus deployments than just about any officer in the U.S. military. A star in the clandestine world of special forces, he had spent years in the shadows hunting terrorist leaders.

And then as the world and warfare changed, he changed with it. He had played a central role in the U.S. military’s efforts to help Ukraine hold off a much larger Russian force, a job that inspired his vision for a new kind of combat that married divebombing drones, robotics and artificial intelligence. Now his fate lay in the hands of Mr. Hegseth, a former Fox News host who had two deployments as an Army officer to Iraq and Afghanistan. Mr. Hegseth had come to the Pentagon vowing to weed out the “small” and “feeble” generals who he believed had failed in those wars.

What played out in the 16 months after the car ride was a clash between Mr. Hegseth and General Donahue’s supporters, who viewed him as a generational talent. That clash, and its outcome, was described to The New York Times by more than 40 people at the Pentagon, in Congress and around the world, nearly all of whom spoke on the condition of anonymity to avoid retribution. It amounts to one of the most consequential chapters in Mr. Hegseth’s campaign to drive out those he sees as out of step with his priorities, a leadership purge that his critics say is driven by ideology, identity and suspicion of those with tenuous ties to former military leaders that he does not like.

And it shows the intensity of the behind-the-scenes battle to save one general. The more General Donahue’s allies pushed, the more Mr. Hegseth’s opposition seemed to harden. The Pentagon declined to answer questions about General Donahue, saying in a statement that all senior military leaders serve at the pleasure of the president and the defense secretary.

In the spring of 2025, General Donahue was commanding ground forces in Europe. Mr. Hegseth was new to the Pentagon. To the extent he was familiar with General Donahue, it was largely through the prism of the Afghanistan withdrawal and a grainy photo that indelibly linked the general to the war’s tragic end. General Donahue was the last U.S. soldier to leave Afghanistan.

As he stepped onto a hulking military cargo plane, an Army photographer snapped his picture using his cellphone camera and night vision device. The green-and-black image rocketed around the world. Senior Pentagon officials said Mr. Hegseth seemed to be fixated on the photo, mistakenly referring to it as a “selfie.”The first item on the card that Mr. Kasper handed to Mr. Hegseth in the car clarified that the photo was not a selfie and that General Donahue had nothing to do with its distribution.

Other bullet points noted that Marines, not General Donahue’s paratroopers, were in charge of the gate where the suicide bombing occurred. The defense secretary glanced at the card and...