Then-national security adviser Michael Flynn and President Trump on arrival at MacDill Air Force Base in Tampa on Feb. 6, 2017, to visit the U.S. Central Command and Special Operations Command. (Mandel Ngan/AFP/Getty Images)

Five days before he resigned as President Trump’s national security adviser, Michael Flynn waxed on about the smooth running of a White House strategy team that, from the outside at least, looked top-heavy with aides close to Trump weighing in on issues under his purview.

“I will tell you that the group of us talk every day,” Flynn said of Stephen K. Bannon, Jared Kushner, Reince Priebus and others who also play senior roles in national security policy. “And we have a great relationship. There’s no angst. There’s no frustration. There’s no sniping or anything like that.”

“I wouldn’t put up with it, personally,” Flynn said in an interview.

In the end, it was the others — who had been investigating him and discussing his future with President Trump for weeks — who apparently decided not to put up with Flynn after he acknowledged he “inadvertently” provided “incomplete information” about his contacts with Russia’s ambassador in Washington.

(Thomas Johnson/The Washington Post)

But in his absence, the National Security Council staff remains very much the team that Flynn — a retired Army lieutenant general and former director of the Defense Intelligence Agency — had been building.

It was unclear whether others would leave or be forced out after him, or whether the changes that Flynn was implementing in the NSC structure would remain in place. Senior officials said that K.T. McFarland, a former Fox News commentator who served in the Nixon and Reagan administrations, wants to and has been asked to remain as deputy national security adviser.

The White House offered no explanation for McFarland’s not being considered to replace her direct boss. Retired Army Lt. Gen. Keith Kellogg, the NSC chief of staff who was an early adviser to Trump’s campaign, has been made acting national security adviser until a permanent replacement is named.

At the head of the list of candidates reportedly under consideration are Robert Harward Jr., a former Navy SEAL who is now a senior executive at aerospace firm Lockheed Martin, and retired Army Gen. David H. Petraeus, the former CIA director. Either one would fit with Trump’s apparent preference for senior military officers.

A number of pending NSC directors, those in charge of regional or policy sub-offices who were personally recruited by Flynn or Kellogg, are awaiting security clearances or other approvals and are unsure whether their job offers still stand or if they should reconsider a decision to join the administration.

“I thought there needed to be somebody there who doesn’t need to get up to speed,” said one of these officials in waiting, a regional expert who spoke on the condition of anonymity because of a lack of information from the White House. “Now, I don’t know what’s happening.”

Most NSC staffers are traditionally on temporary duty from the Defense and State departments and the intelligence agencies. Senior officials said that as many as 60 of those slots are vacant but denied reports that the White House was having trouble recruiting to fill them. Officials said the vacancies were due to rotational and turnover delays in what are normally two-year assignments.

About 75 of a total of more than 200 staffers are direct White House hires. The staff chosen by Flynn is heavily weighted toward the small world of military intelligence officials or strategists who rotated through Iraq and Afghanistan with him over the past decade.

Former naval officer and military intelligence official David Cattler serves as head of regional affairs. Derek Harvey, coordinator for the Middle East, North Africa and the Persian Gulf region, is a former DIA officer who was a longtime adviser to Petraeus when the general was commander of U.S. forces in Iraq. And he worked closely with Petraeus and now-Defense Secretary Jim Mattis at U.S. Central Command in Tampa.

Joel Rayburn and Michael Bell, who hold senior positions under Harvey, had worked closely with Flynn and senior four-star generals such as Petraeus and Stanley McChrystal on the generals’ small internal think tanks in Baghdad and Kabul. Matthew Pottinger, senior director for Asia, is a former journalist and Marine Corps captain who worked directly with Flynn in Afghanistan.

Many also have ties to the military’s universities for midcareer officers. Flynn plucked Bell and Craig Deare, a former Army intelligence officer who is now NSC regional director for the Western Hemisphere, from the tiny six-person leadership team at the College of International Security Affairs at National Defense University.

Their positions, especially overseas, gave them a close-up view of the problems facing troops in war zones — and experience in what one senior NSC official called “real work” — but little experience in dealing with Washington bureaucracies and politics.

Among the few with senior government experience, John Eisenberg, the NSC legal counsel, held senior intelligence-related positions at the Justice Department.

But Flynn had also invited experienced Washington hands to advise him in an informal think tank over the past several weeks They included Stephen Hadley, retired Marine Corps Gen. James Jones and retired Adm. John Poindexter — predecessors as national security advisers in the George W. Bush, Barack Obama and Ronald Reagan administrations. Donald H. Rumsfeld, a defense secretary to George W. Bush, also was included.

The idea, a senior NSC official said, was to make the NSC “a place where we bring in advisers to talk to us about issues — whether it’s Russia or whether it’s China, whether it’s structure or whether it’s climate change. It’s a task force of people that is very flexible.”

Flynn also thought he had a close relationship with Kushner, Trump’s son-in-law, who apparently has taken the White House lead on a number of foreign policy issues, including Mexico and Israel.

“Not everything is going to be lined up like it was for Henry Kissinger or Brent Scowcroft or [Zbigniew] Brzezinski,” Flynn said in the interview, referring to some of his powerful, high-profile predecessors in the job.

Although Obama was criticized for the size of his NSC staff — and legislation passed late last year limits it to no more than 200 — Flynn and his deputies gave no indication in recent interviews that they intended to shrink it. When Obama left, his national security adviser, Susan E. Rice, had reduced the number of nontechnical or administrative staffers from about 230 to about 180.

Instead, Flynn and others indicated that they would restructure the organization to eliminate the wide number of special directorates and deputy special assistants to the White House that many thought had contributed to an overweening, micromanaging NSC.

Greg Jaffe contributed to this report.