Defense Secretary Pete Hegseth has ordered the Pentagon’s inspector general to investigate the “conduct” of retired Joint Chiefs Chairman General Mark Milley — who at times clashed with President Trump during his first term — and determine whether it’s appropriate he should be reduced in rank from his current four stars.

Hegseth also revoked Milley’s security detail and suspended his security clearance.

Even though Milley is retired, he had an ongoing security detail through the Army as a result of Iranian threats in the wake of the 2020 U.S. drone strike that killed Iranian General Qusem Soleimani. Former Secretary of State Mike Pompeo and then National Security Advisor John Bolton recently lost their security details on orders from President Trump, who clashed with them as well.

Hegseth’s chief of staff, Joe Kasper, in explaining the inspector general probe said in a statement on Monday: “Undermining the chain of command is corrosive to our national security, and restoring accountability is a priority for the Defense Department under President Trump’s leadership.”

There was no indication how long the investigation would take.

The decision to strip Milley of his security detail was met with quick criticism from Sen. Jack Reed of Rhode Island, the top Democrat on the Senate Armed Services Committee.

“General Milley and other former Trump Administration officials continue to face credible, deadly threats from Iran because they carried out President Trump’s order to kill Iranian General Soleimani,” Reed said in a statement. “It is unconscionable and recklessly negligent for President Trump and Secretary Hegseth to revoke General Milley’s security detail for their own political satisfaction. The Administration has placed Milley and his family in grave danger, and they have an obligation to immediately restore his federal protection.”

It was not immediately clear exactly what conduct amounted to undermining the chain of command. Milley disagreed with Trump and his aides on a number of issues, from using active-duty troops to restore order in American cities, to the president inquiring about whether the military could shoot unarmed protestors, which Milley and other officials said was an illegal order.

At times, Milley and others convinced Trump to change course on policy. Trump wanted to remove all U.S. troops from Syria in 2018, though Milley persuaded him to have hundreds of troops remain to work with Kurdish forces and deal with a continuing threat from the Islamic State.

Milley, 66, could not be reached for comment.

When he was elected in 2016, Trump chose Milley — then the Army’s top officer — to be his principal military advisor over Air Force General David Goldfein, who then Defense Secretary James Mattis favored. Trump seemed to admire Milley’s boisterous demeanor and outspoken ways. But over time the relationship deteriorated, much like it did with Trump and two other retired generals — Mattis and former White House chief of staff John Kelly.

Right after the George Floyd protests in June 2020, Milley walked with Trump from the White House through Lafayette Square, where law enforcement, aided by National Guard troops, forcibly removed demonstrators. At the time, Milley was wearing camouflage fatigues. As Trump headed through the square to St. John’s Episcopal Church, carrying a bible, Milley peeled off and chatted with National Guard forces, seemingly not wanting to appear in what was clearly a political event. Milley later issued an emotional apology at National Defense University, that officials say incensed Trump.

President Trump walks with Attorney General William Barr (left), Secretary of Defense Mark Esper (center), and Chairman of the Joint Chiefs of Staff Mark A. Milley (right), and others from the White House to visit St. John’s Church after the area was cleared of people protesting the death of George Floyd on June 1, 2020. Milley later issued an emotional apology at National Defense University, that officials say incensed Trump.

Brendan Smialowski/AFP via Getty Images

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Brendan Smialowski/AFP via Getty Images

“As many of you saw, the result of the photograph of me at Lafayette Square last week — that sparked a national debate about the role of the military in civil society,” Milley said in a video address. “I should not have been there. My presence in that moment and in that environment created a perception of the military involved in domestic politics. As a commissioned uniformed officer, it was a mistake that I have learned from, and I sincerely hope we all can learn from it. We who wear the cloth of our nation come from the people of our nation, and we must hold dear the principle of an apolitical military that is so deeply rooted in the very essence of our Republic.”

During this time, Milley also assured Chinese officials that Trump wasn’t looking to attack Beijing during his final weeks in office. Milley has said that call was coordinated with then Defense Secretary Mark Esper and other administration officials, but Trump later said such calls “an act so egregious that, in times gone by, the punishment would have been DEATH.” Officials tell NPR the call already has been investigated and nothing came of it.

 When Milley retired in September, 2023, he reminded those in uniform that they take an oath to the Constitution, against all enemies foreign and domestic, emphasizing the words “all” and “and.”

“We don’t take an oath to a king, or a queen, or to a tyrant or dictator, and we don’t take an oath to a wannabe dictator,” Milley said, in clear reference to Trump. “We don’t take an oath to an individual. We take an oath to the Constitution, and we take an oath to the idea that is America, and we’re willing to die to protect it.”

Before he retired, Milley spoke with Washington Post reporter Bob Woodward for his book about Trump.

“No one has ever been as dangerous to the country as Donald Trump,” the general told Woodward. “Now I realize he’s a total fascist. He is the most dangerous person in this country.”

Such comments could get Milley in trouble, say some civil military experts. It is illegal under military law for any commissioned officer to make “contemptuous words” against the president or other senior officials.

Former President Biden provided pre-emptive pardons to Milley and others, and that applies to federal and military law. But Hegseth appears to be pursuing Milley through administration efforts.

Civil military experts say it’s unusual, maybe even unprecedented, to investigate a former senior officer for conduct that alleges “undermining the chain of command.”

“What is unusual is for a president to punish his own appointee, after the fact, in such a public way at a time when his administration says they’re worried about politicizing the military and weaponizing the Justice Department, ” said Peter Feaver who teaches political science at Duke University.

Roger Petersen, a professor at MIT and author of recent book on the U.S. political dynamics of the Iraq War, Death, Dominance and State-Building, said such a move by the Pentagon could be a strategic effort by the Trump administration to silence any dissent, or contrary advice, within the senior officer ranks.

There are rare times when senior retired officers are recalled to active duty for criminal probes. Back in 2017, Air Force General Arthur Lichte was demoted from four stars to two stars and forfeited $5,000 a month in retirement pay after investigators found he engaged in inappropriate sexual acts while in uniform.

Even before Hegseth’s orders, efforts to distance the Defense Department from Milley’s legacy were being felt at the Pentagon. Within hours of President Trump taking the oath of office last week, a recently installed portrait of General Milley was removed from the walls of one of the building’s corridors.

Federal employee unions and attorneys are urging government workers not to accept an offer from the Trump administration to resign from their jobs by Feb. 6 and be paid through the end of September.

“This ‘fork’ thing is not a buyout,” said Jim Eisenmann, a partner with Alden Law Group who represents federal employees, referring to the “Fork in the Road” subject line that accompanied an email sent to federal workers Tuesday. “It’s not based on any law or regulation or anything really other than an idea they cooked up to get federal employees out of the government.”

The email told employees they had until Feb. 6 to accept the deal, calling it a “deferred resignation program.” Anyone wishing to resign was instructed to reply to the email with the word “resign” and hit “send.”

Almost immediately after the memo hit inboxes, federal workers began sharing their confusion, anger and disbelief on Reddit and elsewhere.

Memo lacked clarity on whether employees who resigned would continue to work

Some of the confusion arose from mixed messaging coming from the U.S. Office of Personnel Management (OPM).

The original OPM memo was unclear on whether employees who choose to resign would be expected to work between now and Sept. 30.

Language included in the memo states: “I understand my employing agency will likely make adjustments in response to my resignation including moving, eliminating, consolidating, reassigning my position and tasks, reducing my official duties, and/or placing me on paid administrative leave until my resignation date.”

One part of the letter that was clear was that employees who accepted the offer would not have to comply with return-to-office requirements.

Many employees took that to mean if they accepted the offer, they would still be expected to work through Sept. 30, but could continue teleworking.

Later, the agency posted an FAQ stating: “Except in rare cases determined by your agency, you are not expected to work.”

An OPM spokesperson confirmed to NPR Tuesday night that the expectation was that employees would be put on paid administrative leave soon after they replied to the memo.

Eisenmann cautioned federal workers to be wary.

“There’s no guarantee other things won’t happen to them between now and then, like they won’t get fired for some other reason or they won’t get laid off pursuant to a reduction in force,” he said.

Some employees even wondered if the email was real

Another red flag for many employees was the fact that the email came directly from OPM, not from their agency heads, which is standard protocol.

Several federal employees told NPR that before last week, they had never received any communications directly from OPM. Some even questioned whether the email was real.

Federal employee unions have condemned the email and are telling their employees not to resign.

Matthew Biggs, president of the International Federation of Professional & Technical Engineers (IFPTE), went as far as to call the email a “resignation threat.”

“It’s written pretty clearly that if you don’t take this thing, this so-called offer, you may not have a job,” he said, pointing to a part of the memo that informs employees who wish to remain in their jobs that “the certainty of your position or agency” is not assured.

IFPTE represents roughly 30,000 federal employees including at NASA, the Army Corps of Engineers, the Department of Defense and the Department of Justice.

Biggs says members who work in areas the memo excludes from the resignation offer, including immigration enforcement and national security, nevertheless received the memo.

“We represent people that do cybersecurity at NASA and other places. We represent scientists, engineers. At the Navy yards, we represent folks that prepare these submarines and these aircraft carriers to go out to sea to support our Navy personnel,” he said.

“What if all these people accepted the offer? What would that do to our national security?”

The Office of Management and Budget has rescinded its call for a pause on federal assistance, according to the agency’s memo shared by Democracy Forward, which led a legal challenge over the effort. But the White House said that only the original memo calling for the freeze had been rescinded.

The new memo says the heads of executive departments and agencies should contact their general counsels “if you have questions about implementing the President’s Executive Orders.”

“Facing legal pressure from our clients and in the wake of a federal judge ruling in our case last evening, the Trump-Vance administration has abandoned OMB’s ordered federal funding freeze,” Democracy Forward said in a statement. “We are proud of our courageous clients — who represent communities across the nation — for going to court to stop the administration’s unlawful actions.”

But Caroline Leavitt, the White House spokeswoman, told reporters that the move simply meant a recession of the memo.

She said efforts to “end the egregious waste of federal funding” will continue. She said the OMB memo has been rescinded “to end any confusion on federal policy created by the court ruling and the dishonest media coverage.” The administration expects that rescinding the memo will end the court case against it.

After widespread confusion from the initially very broad memo calling for a halt in federal assistance, pending review, the White House tried Tuesday to further clarify which programs would not be affected, later specifying that it would not impact Medicaid and SNAP programs, for example.

This latest statement from the White House is likely to add to the confusion rather than clarify it.

Wednesday’s developments follow a federal judge’s order Tuesday that temporarily blocked the effort to pause federal payments for grants and other programs.

Under the original OMB memo obtained by NPR, a temporary pause in funding was set to take effect Tuesday evening, but a senior administration official said that the pause could be as short as a day if an agency determines its programs are in compliance.

The official said the directive should not be interpreted as a full funding freeze. The official, who was not authorized to publicly discuss the internal memo, said that agencies are supposed to review their grants, loans and programs to ensure that they align with the new administration’s priorities.

Administration officials have insisted that the impacts are misunderstood, but the actual text of the memo is far-reaching and the follow-up guidance has been vague. On Tuesday afternoon, the White House issued a fact sheet that said “the pause does not apply across-the-board” and that “any program that provides direct benefits to Americans” — like Social Security, Medicare and food stamps — “is explicitly excluded.”

The spending memo quickly drew legal challenges on Tuesday.

The nonprofit organizations that won the temporary stay Tuesday had claimed in their filing that the memo “fails to explain the source of OMB’s purported legal authority to gut every grant program in the federal government.” The groups also said that the memo failed to consider the interests of grant recipients, “including those to whom money had already been promised.”

Shortly after the decision by the federal Judge Tuesday, a group of attorneys general from 22 states and the District of Columbia filed a separate challenge in federal court.

Congressional reaction

The order provided an early litmus test for just how willing Congressional Republicans would be to cede their power of the purse in deference to the leader of their party – even temporarily.

The order came late Monday night, as House Republicans were gathered at an annual conference in Trump’s backyard at his Doral golf course and resort.

And, by and large, most Congressional Republicans who spoke about the memo said it was a means to an end to implement Trump’s agenda, which is his prerogative.

House Speaker Mike Johnson called it “an application of common sense,” and said it would “be harmless in the end.”

At least one person at the retreat, Rep. Don Bacon, R-Neb., said a heads up would have been helpful.

“How are we supposed to defend [it] if we don’t know what’s coming out and what it really means? And I’ve got constituents calling so it’s just part of life,” he said.

Back on Capitol Hill, North Dakota Sen. Kevin Cramer acknowledged the move questions the authority of Congress, but said he wasn’t concerned.

“[Trump’s] testing his own authority,” Cramer told reporters Tuesday afternoon. “He’s getting some guidance that presidents have more authority than they’d traditionally used.”

Cramer said he supports a pause to reevaluate spending, although he said the move will likely face legal challenges and called the decision a “major test of separation of powers.”

 Idaho Sen. Jim Risch put it more bluntly.

“For all of you who haven’t noticed, this is a different day in Washington, D.C.,” he told reporters Tuesday.