The clearest way to understand the extraordinary nature of the indictment on Thursday of James B. Comey, the former F.B.I. director, is to offer up a simple recitation of the facts.
An inexperienced prosecutor loyal to President Trump, in the job for less than a week, filed criminal charges against one of her boss’s most-reviled opponents. She did so not only at Mr. Trump’s direct command, but also against the urging of both her own subordinates and her predecessor, who had just been fired for raising concerns that there was insufficient evidence to indict.
The charges, which were filed around 7 p.m. in Federal District Court in Alexandria, Va., thrust the Justice Department into perilous new territory. The push for the indictment trampled over the agency’s long tradition of maintaining distance from the White House and resisting political pressure, and it raised the prospect of further arbitrary prosecutions pushed by Mr. Trump against his enemies.
Heightening the break-glass moment, the felony charges against Mr. Comey, who stands accused of making false statements and obstructing justice, were rushed into court as Mr. Trump’s handpicked prosecutor, Lindsey Halligan, hurried to beat the quickly approaching statute of limitations on Mr. Comey’s purported crimes.
The rush to prosecute Mr. Comey was the clearest example yet of how the normal process of justice has been reversed under Mr. Trump, showing how the president came into his second term with targets already in mind and ultimately pressured the Justice Department, over a degree of internal resistance, into finding a way to charge a former director of the F.B.I.
Ms. Halligan, who had been working as a top official in the White House staff secretary’s office and had previously served as a personal lawyer for Mr. Trump, had until now never prosecuted a single case in her career.
Mr. Trump nevertheless appointed her as interim U.S. attorney in the Eastern District of Virginia on Monday afternoon, after publicly berating Attorney General Pam Bondi on Saturday night for not moving more aggressively to prosecute Mr. Comey and two other figures who are longtime targets of his retribution campaign, Letitia James, New York’s attorney general, and Senator Adam B. Schiff, Democrat of California.
Although Ms. Halligan had not been fully briefed on the Comey case before arriving and despite an energetic effort by the career professionals under her to dissuade her from bringing charges, she did exactly that. She was present at the courthouse on Thursday as the case was presented to the grand jury.
In voting to indict, the grand jury judged that the evidence it heard indicated that there were reasonable grounds to believe that Mr. Comey might have committed a crime. But prosecutors have expansive sway over grand juries, and it remains unclear, given the secretive nature of such bodies, how much the grand jurors were aware of the broader circumstances of the case.
Since his first term in the White House, Mr. Trump has wanted prosecutors who would follow through on his desire to use the legal system to punish his perceived enemies, mostly in vain. He often railed to his own advisers and on social media about those he wanted to face charges but who were never prosecuted — among them, Hillary Clinton and former Secretary of State John Kerry.
But in his second term, Mr. Trump has recruited Justice Department officials who share his sense of persecution and has been emboldened by a Supreme Court ruling granting him a broad form of immunity from prosecution. That has allowed him to effectively lay waste to the post-Watergate norms that for nearly half a century have kept presidents from intervening directly in the affairs of the Justice Department.
In the past eight months, Mr. Trump’s Justice Department has summarily fired scores of prosecutors and agents who worked on the criminal cases that he faced while he was out of office. And he has often used those cases as a justification for seeking retributive prosecutions not only against Mr. Comey, but also against other opponents like Ms. James, who pursued a civil case against him in New York, and Mr. Schiff, who while serving in the House led impeachment hearings against him.
But the two-count indictment against Mr. Comey is the most far-reaching and public example of the second Trump administration’s efforts to co-opt the criminal justice system. And while Mr. Trump’s allies see it as an overdue and legitimate effort to hold Mr. Comey accountable for what they consider an abuse of power, it could well go down as a moment when a fundamental democratic norm — that justice is dispensed without regard to political or personal agendas — was cast aside in a dangerous way.
“What we are seeing is the almost wholesale collapse of the Justice Department as an organization based on the rule of law,” said Alan Z. Rozenshtein, a former department official who now teaches at the University of Minnesota Law School.
That Mr. Trump could successfully initiate such a case also increases the potential costs of opposing him, an expansion of presidential power that could chill public dissent across the country.
Even before Mr. Comey was indicted, Mr. Trump and his allies defended bringing charges against him, claiming it was a form of payback for the hardships that Mr. Trump had faced as a defendant and arguing that turnabout in the courts was simply fair play. After the indictment became public, Mr. Trump posted on his social media site, “JUSTICE IN AMERICA!”
But while Mr. Trump was pursued by multiple prosecutors and ultimately indicted in four different venues, there were glaring differences between those investigations and the case against Mr. Comey.
In none of the Trump cases, for example, did President Joseph R. Biden Jr. ever go on social media and publicly declare his desire for Mr. Trump to be prosecuted to millions of followers. Nor did Mr. Biden appoint one of his own personal lawyers to oversee any of the Trump cases, two of which were handled by an independent special counsel, Jack Smith, and two of which were brought by local prosecutors operating beyond the control of the president.
Mr. Trump’s allies were particularly incensed by what was often considered the flimsiest case against Mr. Trump: the one filed by the Manhattan district attorney, Alvin L. Bragg, under a novel legal theory greeted with skepticism by many legal experts.
But even that offers key distinctions with the nascent case against Mr. Comey.
Mr. Bragg, acting independently and with little dissension on his team, filed the indictment against Mr. Trump after nearly a year’s worth of investigation and a monthslong grand jury presentation. Two judges — one state, one federal — evaluated the case and found it sound.
Mr. Bragg’s case ultimately ended with Mr. Trump’s conviction on 34 counts of falsifying business records to cover up unlawful acts related to the 2016 election. Mr. Trump received a mostly symbolic sentence that came with no punishment, and his lawyers are appealing the verdict.
The district attorney also brought that case after declining to go forward with a previous case against Mr. Trump. The earlier case had been advanced by his predecessor and caused significantly more dissent in his office, including the departure of several prosecutors who objected to what they saw as a hasty push to indict Mr. Trump.
Mr. Trump’s allies have suggested that the presence on Mr. Bragg’s team of a former Biden Justice Department official, Matthew Colangelo, indicates that Mr. Biden had somehow influenced the district attorney. But there is no evidence that Mr. Colangelo functioned as an intermediary between the Justice Department and the district attorney’s office. Mr. Colangelo and Mr. Bragg had worked together at the New York attorney general’s office, and Mr. Colangelo took the job in the district attorney’s office after having grown tired of commuting to Washington each week.
There are also shades of the president’s eager targeting of his opponents in Ms. James’s civil investigation into Mr. Trump. While running for attorney general in 2018, Ms. James campaigned in part on pledges to investigate the president, then in his first term. Shortly after being elected, she opened an investigation into his company.
But Ms. James’s inquiry was spurred by comments that Mr. Trump’s former lawyer Michael D. Cohen made before Congress, saying that Mr. Trump had a history of fraudulently exaggerating the value of his properties to receive favorable treatment from lenders.
Her investigation lasted three years, culminating in a lawsuit and civil fraud trial after which Mr. Trump was found liable by a judge for conspiring to manipulate his net worth. The judge assessed him a penalty that, with interest, grew to more than a half-billion dollars.
Recently, an appeals court evaluating the case struck down that penalty, criticized Ms. James for her comments during the 2018 election and allowed the trial judge’s finding of liability to stand only so that the case could proceed to New York’s highest court for review. But earlier in the case, when Mr. Trump’s lawyers sought to convince a federal judge that Ms. James had acted vindictively, they were rebuffed.
Because the circumstances surrounding Mr. Comey’s indictment were significantly more problematic, the case could run into trouble after it goes in front of a judge.
Mr. Comey’s lawyers are likely seek to make hay out of the fact that Ms. Halligan’s predecessor, Erik S. Siebert, chose to quit his job rather than move forward with the case. They could also try to get their hands on — and then exploit to their advantage — a memo written by members of Mr. Siebert’s staff about why an indictment should never have been filed in the first place.
Moreover, Mr. Trump’s own remarks about the case could come back to haunt him.
Over the weekend, Mr. Trump preemptively declared on social media that Mr. Comey, Ms. James and Mr. Schiff were “all guilty as hell, but nothing is going to be done.” A prejudicial statement like that could easily be featured in a motion accusing the Justice Department of taking part in an improperly vindictive prosecution.
Speaking to reporters in the Oval Office on Thursday, Mr. Trump insisted that he had no control over the prosecution.
“I can’t tell you what’s going to happen because I don’t know,” he said. But he soon added: “I can only say that Comey is a bad person. He’s a sick person. I think he’s a sick guy, actually.”
Mr. Comey was indicted about seven hours later.