By late last week, President Trump had decided to fire Gen. Charles Q. Brown Jr., the chairman of the Joint Chiefs of Staff, and replace him with one of two very different candidates, according to two administration officials.

One was Gen. Michael E. Kurilla, a hard-charging Army four-star general who oversees U.S. military operations in the Middle East, one of the Pentagon’s highest-profile assignments.

The other was a little-known retired three-star Air Force officer, Dan Caine, with an unorthodox career path that included time as a fighter pilot, the top military liaison to the C.I.A. and an Air National Guard officer who founded a regional airline in Texas.

Mr. Trump and General Caine met for an hour at the White House on Feb. 14. The president largely made up his mind during a meeting with Defense Secretary Pete Hegseth on Thursday, aides said.

And in a message on social media the next evening, Mr. Trump announced that he had picked General Caine, calling him “an accomplished pilot, national security expert, successful entrepreneur, and a ‘warfighter’ with significant interagency and special operations experience.”

The decision, part of an extraordinary purge at the Pentagon, resulted from intense deliberations over the past two weeks that were tightly held within a small group of senior administration officials, including Mr. Hegseth, Vice President JD Vance and Michael Waltz, the national security adviser, the officials said, speaking on the condition of anonymity to discuss internal discussions.

In Mr. Trump’s first term, he initially seemed to seek a close association with the military’s senior leaders, whom he frequently referred to as “my generals.” That soon gave way to frustration with them as he came to regard them as disloyal.

The president’s deep skepticism prompted him to pass over the more obvious choices, like General Kurilla, to replace General Brown and to pluck General Caine from relative obscurity. His choice, people familiar with his thinking said, was based in part on General Caine’s lack of clear association with the Biden administration and in part on a brief encounter with the general in Iraq six years ago that left Mr. Trump convinced he had the kind of can-do attitude the president sees as making the ideal military officer.

In recent years, Mr. Trump has publicly praised General Caine for telling him during that visit to Iraq that the Islamic State could be defeated far more quickly than more senior advisers had suggested.

Now their rekindled relationship will be tested not only by national security challenges like the war in Ukraine and a rising military threat from China, but also by whether General Caine can live up to Mr. Trump’s expectations of loyalty without politicizing the deliberately apolitical job of providing his best military advice to the commander in chief.

Mr. Trump has fixated on the position of the Joint Chiefs chairman since 2019, when he picked Gen. Mark A. Milley, General Brown’s predecessor. It was a decision the president came to regret.

The president saw General Milley as a grandstander and a traitor. General Milley had publicly apologized for walking with Mr. Trump across Lafayette Square for a photo op after the area had been cleared of peaceful demonstrators following the death of George Floyd in May 2020. The president had asked General Milley why he was not proud that he had accompanied “your president,” and it rankled Mr. Trump that the general swore allegiance to the Constitution, not to him. Their relationship was never the same.

“Trump likes his generals up until the point he doesn’t anymore,” John R. Bolton, the national security adviser in Mr. Trump’s first term, said in an interview.

After Mr. Trump was elected to a second term, word soon spread that he would replace General Brown, a decorated F-16 fighter pilot who in October 2023 became only the second African-American to serve as chairman.

After Mr. Hegseth was narrowly confirmed as defense secretary last month, that likelihood became a near certainty, administration officials said. Mr. Hegseth had previously said General Brown should be fired because of what he called a “woke” focus on diversity, equity and inclusion programs in the military. Mr. Hegseth also questioned whether the general was promoted because of his race, despite his 40 years of service.

Several weeks ago, the search for a new chairman began in earnest, administration officials. Adm. Samuel J. Paparo Jr., the head of U.S. forces in the Indo-Pacific, was briefly considered, among several other initial candidates.

But the list of finalists quickly shortened to General Kurilla and General Caine.

On paper and in conventional thinking, General Kurilla seemed to have the leg up. He was meeting regularly with Mr. Trump and other top national security aides to discuss military priorities in the Middle East. Moreover, General Kurilla, whose tenure at Central Command is expected to wrap up in the next few months, had expressed interest in the job, several current and former military officials said. In the end, General Kurilla seemed too similar to the officers whom Mr. Trump had soured on, aides said.

General Caine, on the other hand, had retired at the end of December after completing the final job in his military career — as the Pentagon’s liaison to the C.I.A. — and joined Shield Capital, a firm in Burlingame, Calif., specializing in cybersecurity and artificial intelligence.

General Caine, 56, who graduated from the Virginia Military Institute in 1990 with a degree in economics, became an F-16 pilot — as his father had been — and was the lead aviator assigned to protect Washington on Sept. 11, 2001, after Qaeda hijackers slammed commercial jets into the Pentagon and the World Trade Center.

His career after that followed an unusual trajectory, as he parlayed one opportunity into another, picking up valuable new skills at each stop as well broadening his vast network of contacts. He was a White House fellow at the Agriculture Department and a counterterrorism specialist on the White House’s Homeland Security Council under President George W. Bush. He served in several highly secretive intelligence and special operations assignments, some in the United States and some overseas, all rare for an Air National Guard officer.

As a part-time Guard officer, General Caine was a co-founder of RISE Air, a regional airline, and managed other private businesses, according to his LinkedIn page and interviews with friends and former colleagues. In his C.I.A. job, he was keenly interested in the intersection of technology and national security, and kept close tabs on American companies that sold cutting-edge technology to Ukraine in its fight against Russia.

But what put him on Mr. Trump’s radar was the president’s short visit to Al Asad air base in western Iraq in late December 2018. In a briefing there, General Caine told the president that the Islamic State was not so tough and could be defeated in a week, not the two years that senior advisers predicted, Mr. Trump recounted in 2019.

And at a Conservative Political Action Conference meeting last year, Mr. Trump said that General Caine put on a Make America Great Again hat while meeting with him in Iraq.

The details of these accounts have shifted over time in Mr. Trump’s frequent retelling of the stories. But Mr. Bolton, who accompanied Mr. Trump on the trip to Iraq, said that General Caine and another senior general briefed the president on a plan to defeat the last remnants of the Islamic State in two to four weeks, not one week. And at no time, he said, did General Caine ever put on a MAGA hat. “No way,” Mr. Bolton said.

In his social media message, Mr. Trump also noted General Caine’s nickname, “Razin,” recalling Mr. Trump’s obsession with former Defense Secretary Jim Mattis’s nickname, “Mad Dog,” a moniker Mr. Mattis hated.

General Caine’s nickname embodied the kind of hell-raiser warrior straight out of central casting that Mr. Trump was looking for in his top general, officials said. He fulfilled a fantasy vision the president has of what generals do, they added.

In his post on Friday, Mr. Trump again praised General Caine’s counterterrorism skills. “During my first term, Razin was instrumental in the complete annihilation of the ISIS caliphate,” the president said. “It was done in record setting time, a matter of weeks. Many so-called military ‘geniuses’ said it would take years to defeat ISIS. General Caine, on the other hand, said it could be done quickly, and he delivered.”

Mr. Trump revealed another reason for his unconventional choice. He said that General Caine had been passed over for promotion by President Joseph R. Biden Jr., a claim that Biden officials said on Sunday they could not address. Aides say that in Mr. Trump’s mind, that perceived snub was a great endorsement, proof that General Caine has no specific loyalty to the previous administration. To Mr. Trump, who views most senior officers as incompetent and politically correct, it also suggests that General Caine has a different mind-set.

Friends and former colleagues say that General Caine, an intensely focused but low-key, self-effacing officer despite his nickname, has been uncomfortable with Mr. Trump’s characterization of his role in defeating the Islamic State. Friends who have known him for decades say they have no idea what his political affiliation is, explaining that the general does not talk about politics. General Caine did not respond to emails requesting comment on Sunday.

But when the White House called a couple of weeks ago as he was preparing to move to Dallas from Washington, friends of General Caine say, he did not hesitate to accept the meetings with Mr. Trump and his top aides, and ultimately the job — out of duty to the country.

Which raises perhaps the most important question for General Caine as he prepares to return to active duty as soon as this week, and get ready for what is expected to be a tough Senate confirmation hearing: Will he give his best unvarnished military advice to Mr. Trump, or tell the president what he wants to hear?

“He was always direct and candid in the interagency, which is no small feat,” Gen. Kenneth F. McKenzie Jr., a former head of Central Command who dealt frequently with General Caine in his C.I.A. job, said on Sunday. “I never saw him as a yes-man.”

Senator Jack Reed of Rhode Island, the senior Democrat on the Armed Services Committee, said in an interview on Sunday that he would press General Caine in his hearing on that central point: “Will he have the ability to speak truth to power?”

Jonathan Swan, Maggie Haberman and Helene Cooper contributed reporting.