Shortly before noon on Monday, the Pentagon announced a highly unusual investigation into Senator Mark Kelly, Democrat of Arizona, who had infuriated President Trump by saying in a video last week that members of the military could refuse to obey illegal orders.
Less than an hour later, a federal judge dismissed indictments that the Trump administration had brought against two of the figures that Mr. Trump had demanded be prosecuted by the Justice Department: James B. Comey, the former F.B.I. director, and Letitia James, New York’s attorney general.
The back-to-back developments demonstrate two important truths that are emerging from Mr. Trump’s retribution campaign as he enters the 11th month of his second term.
The first is that Mr. Trump is facing obstacles as he tries to use the Justice Department to investigate, prosecute and jail those he targets.
The second is that he has other options for pursuing and penalizing those he perceives to have crossed or undermined him.
Not limiting himself to pursuing his foes through the criminal justice system, his administration is using a whole-of-government approach to imposing some kind of penalty on his foes.
Mr. Trump’s political appointees are harnessing a range of departments, obscure agencies and rarely used powers outside the Justice Department to inflict pain.
Samuel Buell, a professor of law at Duke University and former federal prosecutor, said it seemed like Mr. Trump’s top aides were sitting around on a daily basis, saying to themselves, “We have this thing called the executive branch — what can we do with it?”
“It seems like this constant process of discovering levers that can be pulled that either no one was paying attention to in the first term or there were checks in place against those levers being pulled because there were political appointees in place who were unwilling to do it,” Mr. Buell said. “It’s retribution in the form of imposing costs without having thought through the end game.”
The head of the little-known Federal Housing Finance Agency is digging up dirt on Mr. Trump’s enemies’ mortgages.
The Commerce Department is investigating whether Harvard University, which has fought a pressure campaign from Mr. Trump in court, should have its patents — worth hundreds of millions of dollars — taken away. The Health and Human Services Department has begun the process for blocking Harvard from receiving future research grants.
The leader of the Federal Communications Commission has backed Mr. Trump’s criticism of news media organizations, starting investigations into networks and using the commission’s power over media mergers in ways that critics say have extracted concessions on coverage from corporate owners.
And the Office of the Director of National Intelligence and the C.I.A. have declassified intelligence that administration officials claim shows criminality by the administration of former President Barack Obama that now must be investigated.
Mr. Trump has always maintained that he is only rooting out systemic bias and holding his enemies accountable for what he says were unfair prosecutions of him by partisan actors hiding behind a facade of nonpartisanship.
During Mr. Trump’s first term, when he was under scrutiny for his 2016 campaign’s ties to Russia, he repeatedly tried to weaponize the Justice Department, the Internal Revenue Service and the other powers of the federal government against his enemies. Top aides — like his second chief of staff, John F. Kelly — often blocked those efforts, and Mr. Trump never succeeded in having any of his perceived enemies indicted.
While out of office, prosecutors across the country indicted Mr. Trump four times and he openly said that if he returned to office, he would seek vengeance. Mr. Trump understood that simply being targeted by the federal government, given the reputational and financial costs, was penalty in and of itself, even if an investigation never led to a prosecution or conviction. And for his second term, he has surrounded himself with loyalists eager to carry out his wishes rather than restrain him.
Mr. Trump began that effort after being sworn in. But it was unclear how far the Justice Department would go in carrying out his demands and what other forms his retribution campaign would take.
In the first few months of his administration, he used lawsuits, executive orders, withdrawal of security details and public intimidation against media companies, law firms and former officials whom he viewed as disloyal.
By the summer, though, Mr. Trump ramped up the pressure on his Justice Department to indict his rivals like Mr. Comey and Ms. James, and Attorney General Pam Bondi quickly sought to comply.
But Mr. Trump immediately ran into roadblocks.
In the cases of Mr. Comey and Ms. James, career prosecutors concluded that there were no viable charges to be brought, and the top prosecutor overseeing them was pressured into resigning.
Ms. Bondi installed Lindsey Halligan, a former defense lawyer for Mr. Trump who had no experience as a prosecutor, to press ahead in seeking the indictments, which she got from a grand jury. On Monday, a federal judge ruled that Ms. Halligan’s appointment was improper and threw out the charges against Mr. Comey and Ms. James.
But by the time the judge ruled against Ms. Halligan’s appointment on Monday, Defense Secretary Pete Hegseth had opened an entirely new front in Mr. Trump’s retribution campaign.
The Pentagon said it would investigate Mr. Kelly, a former naval officer and astronaut, for “serious allegations of misconduct.”
The announcement suggested that the Pentagon could seek to subject Mr. Kelly to a court-martial for noting publicly in a video with other elected Democratic officials that members of the military did not have to carry out illegal orders — a factual statement that had earlier prompted Mr. Trump to accuse him of sedition. (Retired members of the military can be recalled to active duty and subject to the military justice system for certain crimes.)
“If this is meant to intimidate me and other members of Congress from doing our jobs and holding this administration accountable, it won’t work,” Mr. Kelly said in a statement. “I’ve given too much to this country to be silenced by bullies who care more about their own power than protecting the Constitution.”
By midday on Tuesday, the other elected officials who had recorded the video with Mr. Kelly had been informed that the F.B.I. wanted to speak with them.
Kitty Bennett contributed research.
Michael S. Schmidt is an investigative reporter for The Times covering Washington. His work focuses on tracking and explaining high-profile federal investigations.
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