The confrontation began with a rare admission from within Donald Trump’s own party: something had gone wrong, and senators were no longer willing to simply accept the White House’s word.

In recent days, Republicans on Capitol Hill have joined Democrats in demanding answers about a covert maritime campaign in the Caribbean and eastern Pacific, including a disputed second strike on a suspected narco-boat that may have killed defenseless survivors. The episode has exposed deep unease inside the GOP over questions of war powers, secrecy and the politicization of the military — and placed one of the administration’s central loyalists, Defense Secretary Pete Hegseth, under unusual scrutiny.

At issue is a series of U.S. strikes that began in early September, ostensibly targeting drug trafficking networks and designated terrorist organizations near Venezuela and throughout the region. For weeks, administration officials insisted that allegations of a second strike on survivors from a disabled boat were “fake news.” Mr. Hegseth publicly denied any such operation had taken place.

Then the White House acknowledged that it had.

The reversal inflamed senators who had already been pressing for more transparency. “Either he was lying to us on Sunday or he was incompetent and didn’t know it had happened,” one Republican said pointedly in a clip that quickly circulated online. For a party that has largely fallen in line behind Mr. Trump on national security questions, the suggestion that his defense secretary had misled Congress — or lost control of his own department — marked a striking departure.

Into that breach stepped Senator Alyssa Slotkin of Michigan, a former CIA analyst and Pentagon official who has emerged as one of the administration’s sharpest critics on military oversight. In a recent interview, she described classified briefings on the Caribbean strikes as “unimpressive” and “thin,” saying they fell far short of the detail members of Congress once received about operations in Iraq, Afghanistan or Syria.

“We are technically in an armed conflict with a secret list of groups,” she said, referring to the legal framework the administration is using to justify the attacks. The authority itself, she added, is a classified document that cannot be shared publicly, and when senators asked for basic materials — “You said you videotaped the whole thing. Please provide the video.” — the answer, so far, has been no.

For Ms. Slotkin and a small but growing group of lawmakers from both parties, the pattern echoes earlier chapters in the “global war on terror,” but with an added layer of opacity. “A secret list with a secret legal justification doesn’t send the right message for how we do armed conflict,” she said.

Their concerns are not limited to foreign policy. The senator linked the secret designations overseas to a separate executive order Mr. Trump issued in September on domestic terrorism, which directs the Justice Department to assemble a list of domestic organizations deemed threatening. She warned that, in theory, such a list could encompass groups that are not violent at all — “they can be anti-Christian, they can have a different view of the family” — and could be used to turn the machinery of the federal government against political opponents.

“It’s one thing when we’re talking about drug cartels in the Caribbean,” she said. “It’s another thing when the president has asked the Department of Justice to put together a list of domestic terrorist organizations and then use the weight of the federal government to go after those organizations.”

The debate over secrecy and legal authority has collided with a second, more personal story: the administration’s response to a short video in which Ms. Slotkin and five other veterans in Congress reminded members of the military that their oath is to the Constitution, not to any individual president, and that they are obligated to refuse illegal orders.

The video merely restated existing law. The reaction from Mr. Trump was anything but routine.

According to Ms. Slotkin, the president has repeatedly posted about the lawmakers, at times suggesting they should be investigated, arrested or even hanged. Since those posts, she said, her office and home have been barraged with hundreds — and by now, thousands — of threatening messages. She described graphic voicemails and emails, a bomb threat at her family farm, a suspicious package that brought in the bomb squad and the imposition of round-the-clock security.

“There is one person who’s called for violence here,” she said. “Unfortunately it was the guy at the very top, the president of the United States.”

The senator stressed that she had served in dangerous places before and did not consider herself easily intimidated. But she drew a distinction between personal risk and what it means when threats extend to staff and family members who “didn’t sign up for this.”

If anything, she argued, the reaction has only reinforced her central concern: that the administration is systematically reshaping the military and security apparatus around a narrow political agenda. She pointed to what she called a “purge” of senior officers and watchdogs — generals pushed into early retirement, military lawyers reassigned, inspectors general forced out — and compared it to the kinds of internal housecleaning she once monitored in foreign militaries as a CIA analyst.

“We’d write memos for the president about purges in other militaries,” she said. “Now we’re watching it here.”

For now, senators are pressing for public, unclassified hearings on the Caribbean strikes, including testimony from Admiral Hoya, the commander who reportedly ordered the second attack, and Mr. Hegseth himself. Ms. Slotkin insists that such hearings are not just a matter of congressional privilege but a democratic obligation.

“Unclassified hearings are the way the American people understand what is being prosecuted in their name,” she said. “If we’re going to use lethal force, that’s the basic standard.”

She has also called for a broader reckoning over the domestic use of federal force — from anonymous officers in unmarked uniforms patrolling American cities to renewed talk of invoking the Insurrection Act. In her view, relying on local law enforcement, funded and trained to handle civil disturbances, would be less dangerous than deploying troops and federal tactical units into volatile situations.

“The idea that American citizens would fear people in uniform, not as someone coming to protect them but as a threat, is a strategic and irreversible problem for the United States,” she said.

Whether Congress is prepared to confront that problem remains unclear. The initial signs of Republican resistance to the Caribbean campaign may signal a shift — or simply a momentary break in a long pattern of deference. Ms. Slotkin, for her part, says the test will be whether the Senate follows through.

“We’ve had letters, we’ve had briefings,” she said. “The proof is in what actually happens. Do we bring this into the open, or do we let a secret list and a secret war become the new normal?”