It was an early case of Donald J. Trump seeking retribution through the Justice Department.
In the first year of Mr. Trump’s first presidency, Attorney General Jeff Sessions appointed a top federal prosecutor to review whether the F.B.I. had failed to fully pursue investigations involving Hillary Clinton, including an inquiry into the Clinton Foundation’s ties to a Russian uranium mining operation.
The appointment of the prosecutor, John W. Huber, the U.S. attorney in Utah, was championed by many on the right eager to turn the spotlight away from Mr. Trump’s ties to Moscow. But when Mr. Huber’s work ended years later with no charges or public report, Mr. Trump publicly called him a “garbage disposal unit for important documents.”
As Mr. Trump begins filling out his administration and putting his stamp on Washington again, few issues loom larger than the resilience of the Justice Department’s tradition of independence and its commitment to the rule of law.
Mr. Trump’s grievance-laden campaign rhetoric has left many current and former agency officials fearful that he will seek to turn it into a department of revenge aimed at foes inside and outside government.
They said they worried that Mr. Trump’s past experiences with the Justice Department mean he is less likely this time to settle for an investigation like Mr. Huber’s — one that leads to little punishment or pain for anyone.
In an interview, Mr. Huber characterized his work during Mr. Trump’s first term as a sign of the Justice Department’s ability to withstand any political pressure.
“The department tried very hard to honor its traditions,” Mr. Huber said. “We had strong leadership, and the directions that we followed were reasonable and prudent, and we did our jobs.”
Mr. Huber said that as Mr. Trump prepares to take office again, he remains hopeful that the Justice Department will continue to be stocked with principled leaders who can resist undue political pressure.
“I’m optimistic,” he said, “but like many people in the country I’m also wondering who will be confirmed to lead the department, and that will play a big role in what the department does.”
Mr. Trump’s first term was overshadowed by politically fraught investigations and a kind of bureaucratic Cold War with national security and intelligence officials. Many current and former law enforcement officials say they worry that he will not just pick up where he left off, but intensify past efforts to make the F.B.I. and the Justice Department instruments of his will.
“Based on his past statements, he seems intent on using the Justice Department in a way that breaks with the norms of the past several decades and poses significant issues for the administration of justice and the rule of law,” said Greg Brower, a former U.S. attorney and senior F.B.I. official.
Law enforcement officials are particularly concerned that Mr. Trump seems to be planning to repeat one of the most tumultuous steps of his first term — firing the F.B.I. director. In 2017, Mr. Trump nominated the director, Christopher A. Wray, to a 10-year term to succeed the just-fired James B. Comey. Now, as Mr. Trump gets ready to assume office again, he appears to be preparing to force Mr. Wray out.
Even though Mr. Wray has more than two and a half years left in his term, Vice President-elect JD Vance posted on social media this month that he was busy with interviews for a new F.B.I. director — a statement he later deleted.
Mr. Trump’s already terrible relationship with the F.B.I. only worsened after agents with the bureau searched his Mar-a-Lago home in 2022, finding scores of classified documents that he and his staff had failed to return to the government despite receiving a grand jury subpoena.
The F.B.I. is not alone in facing Mr. Trump’s ire. He has pledged to fire prosecutors, investigate former Representative Liz Cheney and hire a special counsel to investigate the Biden family. Mr. Trump has suggested using the military justice system to pursue Gen. Mark A. Milley, the former chairman of the Joint Chiefs of Staff. He has also publicly threatened to prosecute executives at Google and Facebook.
Since Watergate, federal officials have sought to keep White House politics out of the criminal work that the Justice Department does. Not everything the department does is free of politics — there are plenty of policy areas where its officials take explicit direction from West Wing officials. For decades, however, criminal investigations have generally been off limits to presidents.
Now, Mr. Trump is preparing to reoccupy the White House not just with his agenda, goals and grievances, but with the extra ammunition of a Supreme Court ruling that specifically says he has authority over criminal investigations.
“The president may discuss potential investigations and prosecutions with his attorney general and other Justice Department officials to carry out his constitutional duty,” the court ruled this summer in conferring broad but not fully defined immunity for official acts taken by a president while in office.
Mr. Trump demonstrated his willingness to breach the traditional boundaries between politics and law enforcement in his first term, initiating or supporting a wide range of government investigations into rivals and critics.
As in the case of Mr. Huber’s inquiry, Mr. Trump’s first-term Justice Department would appoint a U.S. attorney to investigate an issue that had been seized on by conservatives. Often those investigations were announced to great fanfare on the right, and quietly fizzled out with little notice. (That approach did, however, prove essential to the department’s effort to unravel the guilty plea made by Mr. Trump’s first national security adviser, Michael T. Flynn.)
When Mr. Trump announced that he had chosen Matt Gaetz, the scandal-plagued former Florida congressman, as his next attorney general, many law enforcement officials saw the selection of someone who had spent years railing against the F.B.I. and the Justice Department as the clearest sign yet of Mr. Trump’s determination to punish both agencies.
Mr. Gaetz quickly backed out, and Mr. Trump has said he will instead nominate Pam Bondi, a longtime ally and former Florida attorney general.
But broad and deep concerns remain within the department that new Trump-chosen leaders may seek to transfer, punish or otherwise retaliate against agents and prosecutors involved in politically sensitive cases. Those include the sprawling investigation of the Jan. 6, 2021, attack on Congress and the special counsel cases against Mr. Trump over his efforts to remain in power after his 2020 loss and his subsequent retention of classified documents.
Civil Service protections make it exceedingly time-consuming and difficult to outright fire an F.B.I. agent or prosecutor even when there is a credible allegation of wrongdoing. But that does not mean there could not be other repercussions for those on Mr. Trump’s enemies list.
The work of the special counsel Jack Smith and his team may well be reviewed by the department’s inspector general. During the first Trump investigation, the inspector general found misconduct by a low-level F.B.I. lawyer, which ultimately led to a guilty plea.
The inspector general’s findings, however, did not go far enough for Mr. Trump and some of his supporters. In a more aggressive iteration of the Huber appointment, the attorney general at the time, William P. Barr, appointed John H. Durham, the U.S. attorney in Connecticut, as special counsel to investigate the agencies that had once investigated the Trump campaign’s possible connections to Russian operatives.
“It was obvious to everyone that the appointment was simply intended to be able to create investigations that could be exploited for political purposes,” Mr. Brower said. The long-running Durham investigation, he said, “shows that in the wrong hands, it’s relatively easy for the Justice Department to start investigations, and leak information about the targets.”
There are still significant checks on such efforts, Mr. Brower said, such as career prosecutors, grand juries, judges and defense lawyers. Mr. Brower added that he hoped “that the new leadership team at the Justice Department will rise to the occasion and effectively preserve the department’s independence and integrity.”
In addition to Ms. Bondi, Mr. Trump has chosen three members of his former criminal defense team for senior roles at the Justice Department. They are likely to be pressed at Senate hearings about where they will draw a line between representing the government and the people of the United States versus their client, the president.
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