GEOFF BENNETT: Overnight, Secretary of Defense Pete Hegseth removed the security detail protecting former Chairman of the Joint Chiefs Mark Milley.

Milley had that security not only as a former chairman, but because he faces ongoing threats for his involvement in a 2020 U.S. drone strike that killed a top Iranian general.

Hegseth also pulled Milley's security clearance and opened an investigation that could end with demoting Milley in retirement.

Here's Nick Schifrin.

NICK SCHIFRIN: In the Pentagon today, where the portrait hung of the 39th Army chief of staff, there is a blank wall.

Where the portrait hung of the 20th chairman of the Joint Chiefs, there is a blank wall.

But now the Trump administration is doing more than painting over Mark Milley's legacy.

It's threatening to punish him for comments like this: GEN. MARK MILLEY, Former Chairman, Joint Chiefs of Staff: We don't take an oath to a king or a queen or a tyrant or a dictator.

And we don't take an oath to a wannabe dictator.

NICK SCHIFRIN: Today, Secretary of Defense Pete Hegseth directed the Defense Department's inspector general to consider an investigation into Milley's -- quote -- "conduct," despite a previous report that exonerated him.

PETE HEGSETH, U.S. Defense Secretary: If you actively undermined the chain of command, as General Milley did under the previous Trump administration, we are going to review those actions administratively inside the Defense Department.

NICK SCHIFRIN: The Pentagon also stripped Milley of his security detail, even though the threat against him from Iran for his role in the death of Quds Force commander Qasem Soleimani is still active, Senate Intelligence Chairman Tom Cotton confirmed this weekend.

SEN. TOM COTTON (R-AR): Yes, I have reviewed the intelligence in the last few days.

The threat to anyone involved in President Trump's strike on Qasem Soleimani is persistent.

It's real.

NICK SCHIFRIN: President Trump chose Milley as his chairman, the senior-most military adviser, but the two eventually clashed, especially over Milley's initial presence with Trump in June 2020...

QUESTION: Is that your Bible?

NICK SCHIFRIN: ... when Trump appeared in Lafayette Square near the White House after protesters demanding justice for George Floyd were cleared by police.

GEN. MARK MILLEY: 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.

NICK SCHIFRIN: After January 6, Milley said he called his Chinese counterpart to avoid conflict.

He called it approved communication.

But Trump in 2023 called it an act so egregious that, in times gone by, the punishment would have been death.

President Biden pardoned Milley on his last day in office, so Milley cannot be court-martialed.

But any decision against him could reduce his rank, even in retirement.

For the "PBS News Hour," I'm Nick Schifrin.

GEOFF BENNETT: And for perspective on this, we turn to Jim McPherson.

He served as undersecretary of the Army and as the Army's general counsel during the first Trump administration.

He also had a 25-year career in the Navy, serving as its top lawyer in uniform.

Thanks for being with us.

And I want to start with your reaction to the Trump White House ending General Milley's security detail, revoking his security clearance, and the Defense Department, now opening an investigation into his background for the apparent offense of his personal disloyalty to Donald Trump.

REAR ADM. JAMES MCPHERSON (RET.

), Former U.S.

Undersecretary of the Army: A lot of mixed emotions, dismay, surprise, sadness.

I think many assumed that the rhetoric during the campaign was just that, it was rhetoric, that the president's promise to be the -- our retribution was rhetoric.

And, unfortunately, the recent spate of executive orders in this action today indicates that it wasn't rhetoric, that we should take him at his word, that what he says regarding getting even with others who he perceives slighted him or criticized him is very real.

Removing General Milley's security detail not only causes threats to him, but to his family as well.

Those threats are ongoing, as we heard.

And those threats came because he performed his duties as an Army officer.

And the country owes him that protection.

To remove that protection now is just shameless.

GEOFF BENNETT: The new defense secretary, Pete Hegseth, was on FOX earlier this evening, and he accused General Milley of breaking the chain of command while serving under President Trump in the first term.

What impact might that assertion, that accusation have on the inspector general investigation?

And how might that impact Hegseth's recommendation to Donald Trump once this investigation ends, whenever it ends?

REAR ADM. JAMES MCPHERSON (RET).

: You have asked the right questions.

First of all, I don't exactly understand how it impacted the chain of command.

General Milley, as the chairman of the Joint Chiefs, was not in an operational chain of command.

The chairman's duties by law are to advise the secretary and the president on military matters.

He doesn't command any forces whatsoever.

So I don't understand how that impacted the chain of command.

Perhaps the secretary misspoke, or the secretary doesn't understand the chain of command.

I think it sends a terrible message.

Not only does it send the message that retribution towards General Milley for what he said or is perceived to have said, but I think the message there is to others who are currently serving on active duty in senior positions that, if you don't toe the line, if you don't line up with what the president and this administration wants, you run the risk of this same retribution that General Milley is now the subject of.

Any good leader wants to surround themselves and empower those who work for them to be in disagreement, to offer alternatives, to challenge assumptions.

That's not what this administration seems to be signaling to its senior military.

What it seems to be signaling is, you better get in line or we're going to come after you.

GEOFF BENNETT: Well, if that's the message that this administration is sending, how do you think serving officers will view it?

How might they receive it and respond?

REAR ADM. JAMES MCPHERSON (RET).

: I think they will be as shocked as I am, first of all, that they're removing that protection, second of all, that they took the photos down.

I can't think of anything more petty than that.

And, finally, that they are threatening his retirement grade.

There's a process for that.

And the process involves the secretary of defense analyzing whatever report he receives and making a recommendation to the president.

Well, it sounds like this secretary has already prejudged that, already has in mind what his recommendation is going to be before there's even been an investigation.

GEOFF BENNETT: What are the practical effects of this type of political retribution?

What are the real negative consequences that could result from this?

REAR ADM. JAMES MCPHERSON (RET).

: I think it's chilling.

It's chilling on the senior military and senior civilians to give their unvarnished recommendations, to criticize assumptions, to offer alternatives.

It creates an atmosphere of just yes-men and -women.

Yes, Mr. President, yes, Mr. Secretary, whatever you want, whatever you think's right, that's what we're going to do.

That's the message that's sent.

And that's the chill that will take effect among the senior leadership in the military.

GEOFF BENNETT: Jim McPherson, former undersecretary of the U.S. Army, thanks again for being with us.

REAR ADM. JAMES MCPHERSON (RET).

: Thank you.