White House to Old Staff: Go Home. Don’t Call Us. We’ll Call You.

When the career staff of the National Security Council popped onto a video call at 11:30 on Wednesday morning, a sense of dread had already settled in.

They knew exactly what President Trump thought of the council: that it was the core of the deep state, whose employees, almost all drawn from the State and Defense Departments or other agencies, had turned against him in his first term.

So it was no surprise when the word dropped. In a terse meeting that lasted just minutes — no questions, please — they were told to pack up and go home. Stay off your email and await further instructions, they were told, and some of you will be invited to apply for your old positions.

By a few minutes after noon, the National Security Council workers, who deal with crises around the world, were drifting out of their offices on a lunch break from which many would not return.

Even so, these may be the lucky ones: No one was fired. Many will simply return to their old agencies and hunt for jobs.

It was an early but dramatic step toward Mr. Trump’s ambitious goal of placing his stamp firmly on the federal bureaucracy. Mr. Trump and his team have planned for months to begin rooting out workers of unknown loyalty — or worse — and replace them with political allies committed to his agenda.

Every new president appoints thousands of new officials across the government, most of them political allies.

But experts say Mr. Trump’s longer-term intentions are clear, telegraphed by an executive order he signed on his first day in office granting himself new power to fire civil servants who since the 1880s have enjoyed special job protections meant to insulate them from shifting partisan winds.

“We’re getting rid of all the cancer,” Mr. Trump said as he signed the executive order, known as Schedule F. “The cancer caused by the Biden administration.”

Schedule F could lead to 50,000 or more firings and “would be a massive reshaping of the federal work force,” said Rachel Augustine Potter, an associate professor at the University of Virginia who studies the federal bureaucracy.

“A lot of the deconstructing of the ‘administrative state’ that Trump talked about in 1.0 was much more talk, but now it seems like they’ve got a plan in action,” she said.

Advocates for federal workers call it a looming crisis, although they add that Mr. Trump will have to fight through legal obstacles to carry out such dramatic changes. The National Treasury Employees Union has already filed a lawsuit challenging the plan.

The Trump administration has “begun the deliberate march to convert our merit-based civil service into a cronyism-based system, but we will fight them every step of the way,” said Senator Chris Van Hollen, Democrat of Maryland.

He singled out the firing of the U.S. Coast Guard commandant, Adm. Linda L. Fagan, by Mr. Trump’s acting Department of Homeland Security chief, who cited an array of causes including supposed mismanagement and an “excessive focus” on diversity within the service.

“That was a very ominous sign of what their plans are,” said Mr. Van Hollen, who said he worked closely with Admiral Fagan after the collapse of a major bridge near Baltimore last March and found her highly qualified.

The meeting with the National Security Council staff exemplified the new dynamic. The council draws on the federal agencies for its talent. And for those chosen, the work at the White House for a year or two is often a huge opportunity to dive into the pinnacle of foreign policy management. They learn to serve presidents of both parties, although it is unclear whether that tradition will continue for now.

Mike Waltz, Mr. Trump’s national security adviser, suggested earlier this month that nothing matters more than his staff’s support for the president’s policies. “Let me be clear: anyone working under President Trump in the NSC will be fully aligned with his America First agenda,” Mr. Waltz wrote on social media. (Mr. Waltz was not on Wednesday’s video call.)

When Mr. Trump first became president, his national security adviser, Michael T. Flynn, gathered the staff in a large auditorium. He laid out his goals; many of the career staff, on assignments that still had six months or a year remaining, stayed around until their temporary assignments ran their course. (In fact, it was Mr. Flynn himself who was fired, in less than a month. Three more national security advisers would follow.)

Of course, when the National Security Council professionals were sent home, operations were bound to slow. Those staff members know the current issues, can log onto the classified computer systems and are the connections back to their home agencies. It wasn’t immediately clear how they would be replaced.

Mr. Trump has said his National Security Council would be smaller. There are fewer deputy national security advisers, and some posts created by President Joseph R. Biden Jr. have been eliminated. But if history is any guide, it will increase in size over time.

Changes have reached senior levels of several other departments and agencies. At the Justice Department, three of the most senior and influential career officials were reassigned to less important posts by Tuesday afternoon, including one who worked on the federal investigation into Mr. Trump’s handling of classified documents between his presidencies.

Some current and former officials said the departures would cost the department valuable expertise and questioned whether the speed of the changes might violate civil service rules.

The new administration also jolted the F.B.I. this week, installing a new acting director and his deputy, bypassing senior agents considered to be in line for those positions.

At the State Department, dozens of senior officials resigned from their posts on Monday at the Trump team’s request, a faster turnover than some diplomats say is typical for the department, particularly given that they do not have immediate replacements. Marco Rubio, the former Florida Republican senator, was sworn in as secretary of state and took his first meetings at the department on Tuesday.

But many career diplomats, well aware that Mr. Trump has called their employer the “Deep State Department,” say things could be worse and have been encouraged by Mr. Rubio’s early comments acknowledging the department’s expertise. Mr. Trump’s first secretary of state, Rex Tillerson, quickly embarked on what he called a “redesign” of the department that featured a proposed 30 percent budget cut, though Congress rebuffed much of that plan.

At the Pentagon, Robert G. Salesses, a longtime midlevel Defense Department official, will serve as acting defense secretary until a new secretary is confirmed by the Senate, according to a White House statement on Monday. The Senate Armed Services Committee voted on Monday to advance the nomination of Pete Hegseth, Mr. Trump’s choice to lead the department, but the full Senate may not vote until later in the week.

Three other career Pentagon officials were tapped to serve as acting secretaries of the Army, Navy and Air Force.

The Pentagon on Tuesday also announced the appointments of 32 midlevel officials who do not require Senate approval. The officials, including chiefs of staff, policy specialists, lawyers and media officers, represent a skeletal team to begin carrying out Mr. Trump’s directives until numerous political appointees can be confirmed over time.

By Wednesday there were no signs of widespread dismissals within the Defense Department.

Mr. Salesses, a retired Marine Corps officer, is the deputy director of the Washington headquarters services, which is focused on human resources, facilities and resource management. He has also served in top Defense Department policy jobs overseeing the Pentagon’s support for homeland defense missions and domestic crisis management.

For many Pentagon officials, the week’s most dramatic development has been the White House-ordered removal from the building of a portrait of Gen. Mark A. Milley, who served as chairman of the Joint Chiefs of Staff under Mr. Trump. After his retirement, Mr. Milley publicly denounced Mr. Trump as a danger to the nation and a “fascist to the core.”

Some military and civilian officials who have worked under General Milley are worried about whether they might be targeted in any loyalty purge.

The Transportation Safety administrator, David Pekoske, was also asked to step down on Monday. He was appointed by Mr. Trump but was kept on by Mr. Biden. Colleagues had expected him to serve out a five-year term ending in 2027 and to double as the acting chief of the Department of Homeland Security.

Devlin Barrett, Helene Cooper, Adam Goldman, Eric Schmitt, Mark Walker and Edward Wong contributed reporting.