Mr. Bove wrote that the demand had nothing to do with the strength of the evidence against the mayor or legal theories in the case. Rather, he said the charges would interfere with Mr. Adams’s ability “to devote full attention and resources to the illegal immigration and violent crime that escalated under the policies” of the Biden administration.

After Ms. Sassoon’s resignation as head of the Southern District of New York and those of at least seven Justice Department officials, Mr. Bove himself signed a motion on Friday asking the judge to dismiss the case.

It remains to be seen how the judge, Dale E. Ho of Federal District Court in Manhattan, will respond.

“Judge Ho could say this is a politically motivated decision and it affronts the grand jury process and the integrity of the court,” said Stephen Gillers, a professor of legal ethics at New York University School of Law.

Professor Gillers said Judge Ho could decide that the government’s justification for seeking dismissal was inadequate. The government would almost certainly appeal, he said.

Since Mr. Adams was indicted in September, the U.S. attorney’s office for the Southern District of New York has vigorously prosecuted the charges against the mayor in court, continuing to do so after the Trump administration elevated Ms. Sassoon last month to lead the office. Judge Ho has repeatedly denied Mr. Adams’s requests to have the case dismissed.

Ms. Sassoon, in a letter Thursday to the attorney general, noted that Judge Ho had “stressed transparency” during the case. She said the judge was likely to conduct a rigorous and lengthy court inquiry that could be “detrimental to the department’s reputation, regardless of outcome.”

In her letter, Ms. Sassoon said that Mr. Bove’s suggestion that the issue was merely removing an obstacle to the mayor’s ability to help with federal immigration enforcement did not bear scrutiny.

“Rather than be rewarded,” Ms. Sassoon said, “Adams’s advocacy should be called out for what it is: an improper offer of immigration enforcement assistance in exchange for a dismissal of his case.”

Professor Gillers said Mr. Bove’s rationale for seeking dismissal of the charges would not sit well with the judge.

“Judge Ho will not accept that — should not accept that — as the justification for throwing out a grand jury decision to indict.”

Judge Ho, a graduate of Yale Law School, has been on the bench only a short time: He was appointed by President Joseph R. Biden Jr. and narrowly confirmed by the Senate in 2023. But few judges of any tenure have faced a situation like the one he confronts now.

In the past, even judges who have expressed reservations about a government request to drop charges felt compelled to go along, given their limited say.

The issue arose in 2020 during Mr. Trump’s first term, in the prosecution of Michael T. Flynn, his national security adviser. That year, Mr. Flynn, who had pleaded guilty to lying to the F.B.I., sought to withdraw his plea, and federal prosecutors in Washington moved to dismiss the indictment against him. When the judge overseeing the case, Emmet G. Sullivan, did not immediately grant the dismissal, Mr. Flynn took his argument to the U.S. Court of Appeals for the District of Columbia.

In a June 2020 decision, a three-judge panel of that court noted that “decisions to dismiss pending criminal charges” were squarely within a prosecutor’s purview and that circumstances in which a judge could intervene were limited. Their ruling was overturned, but the precedent that informed it stands.

In a more recent case, federal prosecutors in Washington last month moved to dismiss an indictment against two men associated with the Proud Boys. They received clemency from Mr. Trump after pleading guilty in connection with the Jan. 6, 2021, attack on the Capitol.

The judge, Beryl A. Howell, wrote a scathing opinion criticizing the government’s rationale for asking to drop the charges — that Mr. Trump’s pardons and commutations for Jan. 6 offenses had ended “a grave national injustice that has been perpetrated upon the American people.”

“This court cannot let stand the revisionist myth relayed in this presidential pronouncement,” Judge Howell wrote, noting that the defendants had admitted to their conduct and had been afforded every protection guaranteed by the Constitution.

But Judge Howell said there were no “legitimate grounds” to deny the government’s motion, and she granted the request to dismiss the indictment.

Mr. Bove, whose order specified that the decision to dismiss the case had nothing do with its legal strengths, was ultimately compelled to sign the motion himself, along with two other Washington prosecutors, Edward Sullivan and Antoinette T. Bacon.

The reason he gave the judge was the same as he gave the New York prosecutors: that the prosecution would hinder Mr. Adams’s ability to cooperate with the Trump administration’s immigration policies. It was a highly unusual rationale for dismissing a criminal case, which is typically evaluated on the basis of the facts and the law. The abnormality was underscored by Mr. Bove’s difficulty in finding a prosecutor willing to affix a name to the filing.

Now attention will turn to Dale E. Ho, the judge who is overseeing the case in Manhattan federal court.

Mr. Adams was indicted last year on five counts, including bribery, fraud and soliciting illegal foreign campaign donations. He pleaded not guilty and was scheduled for trial in April. Ms. Sassoon, in a letter to the attorney general this week, said that prosecutors were prepared to bring an additional charge that would accuse him of destroying evidence and instructing others to do the same.

A lawyer for Mr. Adams, Alex Spiro, called that a false claim. He said that if prosecutors had proof that the mayor destroyed evidence “they would have brought those charges — as they continually threatened to do.”

Under the law, judges may question a prosecutor’s decision to seek a dismissal of charges, but they almost always grant such requests. Stephen Gillers, a legal ethics professor at New York University School of Law, said that Judge Ho could decide that the Adams case was the rare exception, that the government’s justification was inadequate.

Ordinarily it is the responsibility of the U.S. attorney whose office prosecutes a case to move for its dismissal. But Ms. Sassoon, 38, quit Thursday after telling the attorney general that she would not obey an order that had no valid basis.

In her letter to the attorney general, Pam Bondi, Ms. Sassoon characterized the order as a quid pro quo — dropping the charges in exchange for the mayor’s support of Mr. Trump’s political program.

“I cannot agree to seek a dismissal driven by improper considerations,” Ms. Sassoon wrote.

The Manhattan federal prosecutors who had been involved in Mr. Adams’s case sent a letter to Judge Ho on Friday evening indicating they were withdrawing.

They included Hagan Scotten, the lead prosecutor, who had already resigned from the Southern District in protest of Mr. Bove’s order.

In a scathing resignation letter, Mr. Scotten wrote that any federal prosecutor “would know that our laws and traditions do not allow using the prosecutorial power to influence other citizens, much less elected officials.”

He added: “If no lawyer within earshot of the president is willing to give him that advice, then I expect you will eventually find someone who is enough of a fool, or enough of a coward, to file your motion. But it was never going to be me.”

Three others also left the case: Celia V. Cohen, Andrew Rohrbach and Derek Wikstrom.

In his directive to Ms. Sassoon, Mr. Bove said that he had told the mayor’s lawyers that the government was not offering “to exchange dismissal of a criminal case for Adams’s assistance on immigration enforcement.” But on Thursday, hours after Ms. Sassoon quit, the mayor said he would allow federal immigration authorities to operate within the Rikers Island jail complex.

Ms. Sassoon said in court papers last month that there was “concrete evidence” of crimes by Mr. Adams, and that his claims that his prosecution was politically motivated were meant to divert attention “from the evidence of his guilt.”

For days, Manhattan prosecutors had been watching to see how Ms. Sassoon would handle the Justice Department’s directive to drop the charges; she and other top prosecutors had traveled to Washington recently to meet with department officials to discuss the issue in person.

The Trump administration last month elevated Ms. Sassoon, a veteran prosecutor, to head the U.S. attorney’s office for the Southern District of New York while President Trump’s choice for the post, Jay Clayton, awaited Senate confirmation.

In Mr. Bove’s letter accepting her resignation, he blasted her handling of the case and decision to disobey his order.

He told her that the prosecutors who had worked on the case against Mr. Adams were being placed on administrative leave too, and said they and Ms. Sassoon would be investigated by the attorney general and the Justice Department’s internal investigative arm.

Matthew Podolsky, who had been Ms. Sassoon’s deputy, is now the acting U.S. attorney.

The indictment against Mr. Adams was announced in September by the U.S. attorney who led the office during the Biden administration, Damian Williams. Mr. Adams, a Democrat, has claimed that he was targeted because of his criticism of the administration over the migrant crisis — an assertion the Southern District has rebutted, noting that the investigation began well before the mayor made those comments.

Mr. Adams has praised parts of Mr. Trump’s agenda, visited him near his Mar-a-Lago compound and attended his inauguration a few days later. Mr. Trump had floated the possibility of a pardon, and criticized Mr. Adams’s prosecution, saying the mayor had been “treated pretty unfairly.”

The prosecutors’ leadership of the Southern District, which is widely seen as the nation’s most prestigious U.S. attorney’s office, dates back nearly half a century. They oversaw trials involving terrorism, Wall Street fraud, the mafia and Russian espionage.

The Southern District has a reputation for independence and for fending off interference from officials in Washington. The Justice Department’s attempt to stop it from prosecuting Mayor Eric Adams has mightily tested that norm.

The seven former Southern District U.S. attorneys include Mary Jo White, the first woman to hold the post, and who served from 1993 to 2002; and Robert B. Fiske Jr., whoserved from 1976 to 1980.

In their statement, the former U.S. attorneys sharply criticized the Justice Department’s intention to investigate Ms. Sassoon and some of the career prosecutors who served alongside her. They called the prospect of such investigations “a stark departure from those traditions that should concern everyone committed to the pursuit of justice without fear or favor.”

In a letter to Ms. Sassoon on Thursday, Emil Bove III, the deputy attorney general, said the investigations would be carried out by the department’s Office of Professional Responsibility and the office of the attorney general, under a new executive order by Mr. Trump titled “Ending the Weaponization of the Federal Government.”

The other former U.S. attorneys who signed the letter were John S. Martin Jr., James B. Comey, David N. Kelley, Geoffrey Berman and Audrey Strauss.

Mr. Adams, a Democrat, said that he was happy to be working with Mr. Homan to target immigrants who are accused of serious crimes.

“I’m really pleased to have this collaboration because it was almost as though I was crying out in the wind and this administration heard it,” Mr. Adams said, referring to his earlier pleas to the Biden administration for more assistance.

Dr. McGraw, better known as Dr. Phil, has seen his prominence in Mr. Trump’s orbit rise, and he recently accompanied immigration agents during an enforcement operation in Chicago.

Mr. Adams has said that he is opposed to mass deportations and only wants to target people who have committed crimes. But Mr. Homan warned that there would be collateral damage. “If you’re going to force us into the neighborhoods, we’ll find the bad guy,” he said. “But if he’s with others who are in the country illegally, they’re coming, too.”

Mr. Homan said that he had found common ground with Mr. Adams over allowing federal immigration authorities to return to the Rikers Island jail complex. But he said they did not agree on everything.

“We’re going to have arguments,” Mr. Homan said. “This isn’t a perfect relationship. But it’s the start of a good relationship.”

Dr. Phil responded with a joke. “I’ll do therapy on you like an old married couple,” he said, as Mr. Adams laughed.

Ms. Sassoon, who was then serving as the acting U.S. attorney for the Southern District of New York, cited conversations during a meeting she had in late January with Mr. Adams’s lawyers and Emil Bove, the Justice Department official who ordered her to drop the case in a memo on Monday. Mr. Bove’s memo cited immigration enforcement as one of the reasons the prosecution should be killed.

Ms. Sassoon said in the letter that during the meeting, Mr. Adams’s lawyers said the mayor could assist with immigration enforcement “only if the indictment were dismissed.” She added that Mr. Bove scolded one of her prosecutors for taking notes on the conversation and had them confiscated when the meeting ended.

Although Mr. Bove has denied trading the case for the enforcement of an immigration crackdown, as has the mayor and his lawyers, “that is the nature of the bargain laid bare in Mr. Bove’s memo,” Ms. Sassoon wrote.

Ms. Sassoon’s accusation injects a measure of irony into the internal debate over how to handle Mr. Adams’s case: One of the crimes he was charged with committing was trading official action for personal benefit. Federal prosecutors said he had accepted luxury travel in exchange for pressuring the New York Fire Department to sign off on opening a high-rise consulate building for the Turkish government.

Ms. Sassoon noted in her letter that prosecutorial power cannot be used to coerce defendants, saying that could be considered legal misconduct. Hagan Scotten, the lead prosecutor on the Adams case — who was put on leave before he resigned — went further in his resignation letter to Mr. Bove, calling such behavior illegal.

“Any assistant U.S. attorney would know that our laws and traditions do not allow using the prosecutorial power to influence other citizens, much less elected officials, in this way,” he wrote.

Even if it could be proven that Mr. Adams and Mr. Bove had made a deal like that, it is not clear that the arrangement would be a prosecutable crime. But Carrie H. Cohen, a former federal and state prosecutor in New York who brought many corruption cases, said that regardless of whether such a deal fits neatly within the definition of bribery, it would unquestionably be wrong.

“Is it appropriate to say, ‘I will take official actions related to immigration policy for personal gain’?” said Ms. Cohen, now a defense lawyer. “No. That is what the bribery laws are supposed to prevent.”

Jessica Tillipman, an associate dean at George Washington University Law School, said the dismissal of charges could theoretically be considered something of value in a bribery case, but she added that it was not a case the Justice Department seemed likely to bring any time soon.

“Do I think it would ever be prosecuted like that? No,” Ms. Tillipman said. “Maybe in a future administration.”

Ms. Hochul, a Democrat, called the allegations “extremely concerning and serious,” and was soliciting views from powerful fellow Democrats and her closest advisers.

But five people familiar with the governor’s thinking said that Ms. Hochul favored a deliberative path. She had not yet concluded that Mr. Adams was posing the kind of urgent threat to the city’s governance to warrant an intervention that could unleash far-reaching practical, legal and political consequences, according to the people, who were not authorized to discuss her position publicly.

While the State Constitution clearly gives the governor the power to remove the mayor, history offers little guidance for how such a move might unfold. No governor since Franklin D. Roosevelt has even tried to use the removal power against a sitting New York City mayor, and even that almost century-old action never reached a conclusion.

Mr. Adams and his defenders could challenge any action by the governor in court, or at least demand a right to defend themselves against a removal proceeding. A move by Ms. Hochul would also almost certainly anger the Trump administration at a time when she is trying to persuade the president not to undo the state’s new congestion pricing program.

It could also set off a string of political events that could lead to one of her top rivals, former Gov. Andrew M. Cuomo, becoming mayor.

Ms. Hochul signaled some of her concerns Thursday night in an interview on MSNBC.

“I cannot, as the governor of this state, have a knee-jerk, politically motivated reaction like a lot of other people are saying right now,” she said. “I have to do what’s smart, what’s right, and I’m consulting with other leaders in government at this time.”

She added: “You got to have one sane person in this state who can cut through all the crap and say, ‘What does my responsibility guide me to do?’”

The governor’s thinking may change. The drama swirling around Mr. Adams has unfolded rapidly this week.

Top Justice Department officials on Monday ordered prosecutors to dismiss the charges against Mr. Adams, including a bribery count. By Thursday, the U.S. attorney in Manhattan, Danielle R. Sassoon, and several other department officials resigned rather than obey the order, and they asserted that there had been a quid pro quo. (Mr. Adams strongly disputed that.)

Former allies of the mayor publicly worried that he was now governing in Mr. Trump’s interest, not the city’s — a concern that deepened after Mr. Adams met on Thursday with Mr. Trump’s border czar, Thomas Homan, and announced an executive order that would allow federal immigration authorities into the Rikers Island jail complex.

The sequence of events prompted more New York officials, including Lt. Gov. Antonio Delgado, to either call for Mr. Adams to resign or be removed.

“As long as Trump wields this leverage over Adams, the city is endangered,” Representative Alexandria Ocasio-Cortez said in a post on social media. “We cannot be governed under coercion. If Adams won’t resign, he must be removed.”

Initiating the removal of Mr. Adams, who has always insisted he was innocent of the charges, would set off an extraordinary and unpredictable course of events. A mayor of New York City has never been removed by the governor. The closest precedent occurred in 1931, when Roosevelt pushed to remove Mayor Jimmy Walker. The matter was never formally tested, however: Fourteen days of hearings were held, but Mr. Walker eventually resigned and moved to Europe.

Jerry H. Goldfeder, a longtime election lawyer who teaches at Fordham Law School, said in an interview that Mr. Roosevelt allowed Mr. Walker “free rein” to call witnesses and introduce evidence to defend himself. If Ms. Hochul were to play this card, he said, she would be on firm ground so long as Mr. Adams was given clear reasons for his removal and the chance to offer a defense.

“If the governor is going to charge a mayor with the kind of conduct that she believes requires removal, she should have an expansive view of what due process rights he’s entitled to,” Mr. Goldfeder said.

Roosevelt’s ability to call the hearings stemmed from the State Constitution and a two-sentence section in the City Charter that states: “The mayor may be removed from office by the governor upon charges and after service upon him of a copy of the charges and an opportunity to be heard in his defense.”

“I think her main consideration is likely to be the disruption to city and state government, versus waiting until November,” said Evan A. Davis, a onetime counsel to Gov. Mario M. Cuomo. Mr. Davis has previously called on Ms. Hochul to use this power.

“The closer you get to November, obviously the less reason there is to go through all the rigmarole you would have to go through,” he said.

If Ms. Hochul were to remove Mr. Adams, she would be able to suspend him for “a period not exceeding 30 days.” Mr. Walker’s hearings might offer some inspiration but “there is nothing at all mechanical about it,” Mr. Davis said. “There is no established process you could just fall right into and set in motion.”

Jumaane Williams, the city’s public advocate, who would become the acting mayor if Mr. Adams were to resign or be removed, said on Friday that he wished the mayor would do what is best for the city and step aside.

Mr. Goldfeder wrote in a law paper in the fall that there was little question that Ms. Hochul had the power to remove Mr. Adams, but “a governor who chooses to exercise the power of removal has no clear guideposts, and must navigate proceedings with care.”

Ms. Hochul faced a less intense version of this pressure in the fall. After Mr. Adams was first charged, he and the governor spoke multiple times, and she was able to push him into cutting ties with several aides who were also enmeshed in scandal. She instructed her legal team to study how the removal process might work but did not go further at the time.

“When the allegations came out last September and the city was in chaos, I said, ‘I will intercede, work with the mayor to get rid of a lot of people who are under indictment, calm it down, bring in a new police chief commissioner,’” Ms. Hochul told Rachel Maddow of MSNBC.

“Our subways are safer, people are feeling better around the city, more people are coming back,” the governor said. “I don’t want our rebirth to be stopped by this.”

Looming over this is a set of political risks for Ms. Hochul. Mr. Adams would be all but certain to make a removal hearing about white elected officials targeting the city’s second Black mayor. His standing among this key group of voters appears to be faltering, though.

The Rev. Al Sharpton, a longstanding ally of the mayor’s who wields considerable influence among his political base, was adamant in the fall that the governor should not remove Mr. Adams. But in an interview on Friday, he said he thought “the Trump people have compromised him. And I think that he’s put the city where we are hostage.”

Emma Fitzsimmons and Dana Rubinstein contributed reporting.

But the attorney general at the time, Elliot L. Richardson, refused to fire Mr. Cox and chose to resign instead. The deputy attorney general, William D. Ruckelshaus, also refused to do so and was fired. The order was eventually carried out by Robert Bork, the solicitor general. (Mr. Nixon eventually resigned.)

What happened this week in the Adams case was the Saturday Night Massacre “on steroids,” Steve Vladeck, a law professor at Georgetown University, wrote on Thursday.

In both instances, there was a “clash between the president’s personal preferences and what Justice Department lawyers think the rule of law requires,” Mr. Vladeck said in an interview on Friday.

Danielle R. Sassoon, the top federal prosecutor in Manhattan, chose to offer her resignation on Thursday instead of dropping the Adams case. The lead prosecutor on the investigation, Hagan Scotten, has also announced his resignation.

Ms. Sassoon has accused the mayor’s lawyers of urging “what amounted to a quid pro quo” of assistance with the president’s immigration crackdown if the mayor’s case is dismissed. On Thursday afternoon, Mr. Trump told reporters in the Oval Office that he had not asked for the case to be dropped.

But experts still see parallels with Mr. Nixon.

“You have a sword of Damocles hanging over the mayor in the event that he does not cooperate with the president and his immigration policy objectives,” said Juliet Sorensen, a former federal prosecutor and professor at Loyola University Chicago School of Law who has also written a case book on public corruption and the law.

She said that it could be inferred by the directive that the mayor’s indictment could be reinstated. Mr. Nixon wanted to stave off the Watergate investigation and now, she said, Mr. Trump wants Mr. Adams to cooperate with his immigration policy agenda.

She also said that in both cases, career lawyers resigned in protest “as a matter of professional responsibility and refused to get in line behind a blatantly political objective.”

Since 1973, there have been plenty of examples of lawyers resigning rather than following directives given by their superiors, Mr. Vladeck said.

“But we haven’t seen this sort of large-scale resignation all because the lawyers refuse to do something the political masters wanted them to do since that Saturday night in 1973,” he said.

Garrett Graff, who has written a book about Watergate, said that comparisons to the Saturday Night Massacre were “inescapable,” and even argued that what happened this week was worse.

“Nixon’s fight with the special prosecutor was a question of presidential power and executive authority,” Mr. Graff said. What is happening now, he said, is “even more fundamentally corrupting for the foundation and principles of the rule of law in American life, which is a Justice Department dropping legitimate charges against a public official in exchange for political favors.”

Mr. Vladeck said the resignations were likely to influence what happened to the mayor’s case and could lead courts to question the Justice Department’s credibility. The Adams case is being overseen by Judge Dale E. Ho of Federal District Court in Manhattan.

The resignations could also make it difficult for the department to recruit high-powered lawyers like Ms. Sassoon and her colleagues, Mr. Vladeck said.

“These are the people you want in those jobs,” he said. “If you’re coming out of law school and you’re interested in a career public service, this is a flashing red light about whether you really want to go work for this particular department.”

Sharply differing interpretations of the classic 85-year-old speech, “The Federal Prosecutor,” figured prominently in an extraordinary exchange of letters on Thursday that led to the resignation of Danielle R. Sassoon after she refused to carry out the Trump administration’s command to drop the corruption prosecution of New York City’s mayor, Eric Adams.

The two views reflect a schism in conservative legal thought over how prosecutors, now working for a Trump-led Justice Department, should balance their duty to obey orders from superiors with their obligation to follow their best understanding of the law. One view emphasizes caution, deliberation, and independent and decentralized judgment, while the other values top-down vigor in the service of policy goals that can seem transactional if not unprincipled.

The split could reshape not only the relationship between federal prosecutors around the country and their bosses in Washington, but also the limited but real discretion enjoyed by all sorts of other officials throughout the government. Thursday’s events, in other words, are emblematic of the ethos of the second Trump administration, one that requires federal workers to fall into line or be fired.

Ms. Sassoon, whose resignation led to a cascade of others, cited Mr. Jackson’s speech to argue that the administration’s directive was not the product of a good-faith difference of opinion but an assault on the rule of law.

She wrote that she could not ethically ask a judge to dismiss a case when she did not believe the law supported the move and quoted Mr. Jackson: “The prosecutor at his best is one of the most beneficent forces in our society; when he acts from malice or other base motives, he is one of the worst.”

Emil Bove III, who represented President Trump in three criminal cases and now serves as acting deputy attorney general, responded in accepting Ms. Sassoon’s resignation that federal prosecutors, like other members of the executive branch, are tasked with advancing the president’s goals. The case against Mr. Adams, Mr. Bove wrote, interfered with the mayor’s ability to address two of the administration’s key priorities, immigration and violent crime.

“You lost sight of the oath that you took when you started at the Department of Justice by suggesting that you retain discretion to interpret the Constitution in a manner inconsistent with the policies of a democratically elected president,” he wrote.

Mr. Jackson was 48 and just three months into his tenure as attorney general when he gave his speech, which is universally acknowledged to be the classic account of the prosecutor’s role. He had earlier served as solicitor general, the federal government’s top appellate lawyer, and he would go on, in addition to sitting on the Supreme Court, to be a prosecutor at the Nuremberg trials after World War II.

A central point of his speech was that U.S. attorneys, the top federal law enforcement officials in the nation’s 94 judicial districts, should generally have the last word. Local prosecutors know the facts on the ground, the judges they appear before, the jury pool and “local sentiment and opinion,” Mr. Jackson wrote.

“It is an unusual case,” Mr. Jackson wrote, “in which his judgment should be overruled.”

Ms. Sassoon wrote that the decision to dismiss the charges against Mr. Adams over her objections was not the product of the sort of sober deliberation that should warrant an exception to that general approach. She said Mr. Adams’s lawyers had urged what she characterized as a “quid pro quo” in which the mayor would support Mr. Trump’s priorities if the indictment were dismissed.

“I remain baffled,” she wrote, “by the rushed and superficial process by which this decision was reached, in seeming collaboration with Adams’s counsel and without my direct input on the ultimate stated rationales for dismissal.”

Ms. Sassoon’s interpretation of Mr. Jackson’s words is the conventional one, and it is a reflection of her credentials and place in the conservative legal community. A graduate of Harvard College and Yale Law School, she served as a law clerk to two leading conservative jurists, Judge J. Harvie Wilkinson of the U.S. Court of Appeals for the Fourth Circuit, in Richmond, Va., and Justice Antonin Scalia.

John Q. Barrett, a law professor at St. John’s University who is writing a biography of Justice Jackson, said there was little doubt about how he would have viewed the Justice Department’s handling of the Adams case. “Pretty obviously he would be dismayed and appalled,” Professor Barrett said.

Mr. Bove, however, drew a different lesson from the Jackson speech in his letter accepting Ms. Sassoon’s resignation, writing that there was “great irony” in Ms. Sassoon’s invocation of the speech.

“His remarks are unquestionably relevant here, but not in the way you have suggested,” he wrote.

Mr. Bove, seeming to ignore the main theme of the speech, quoted snippets from it.

“Jackson warned that ‘some measure of centralized control’ over federal prosecutors was ‘necessary,’” he wrote.

“The senior leadership of the Justice Department exercises that control,” Mr. Bove went on. “Moreover, one of Jackson’s concerns was that ‘the most dangerous power of the prosecutor’ arises from the risk that the prosecutor would ‘pick people that he thinks he should get, rather than pick cases that need to be prosecuted.’”

Judge Wilkinson, who was among the judges President George W. Bush considered naming to the Supreme Court, said on Friday that Ms. Sassoon had been an exemplary law clerk.

“While I do not know the particulars in this case,” he said, “what I do know is that Danielle possesses great integrity and courage, which has always made me proud.”

In a tribute after Justice Scalia died in 2016, Ms. Sassoon wrote that his loyalty was to neutral legal principles.

“Justice Scalia was devoted to the integrity of reasoning and ideas,” Ms. Sassoon wrote. “He cared deeply about logic, process and the rules that undergirded particular outcomes — those rules would endure and be the tools used by lower courts to decide future cases.”

Ms. Sassoon added, in a passage that seemed to anticipate her resignation, that Justice Scalia “lacked the abundant caution that plagues today’s media-conscious politicians, judges and lawyers.”

In instructing Ms. Sassoon on Monday to dismiss the charges against Mr. Adams, Mr. Bove invoked a different set of values, one rooted in politics and payback.

“It cannot be ignored that Mayor Adams criticized the prior administration’s immigration policies before the charges were filed,” Mr. Bove wrote.

In a footnote, Mr. Bove denied offering an explicit deal to Mr. Adams’s lawyer, writing that he said at a meeting last month that “the government is not offering to exchange dismissal of a criminal case for Adams’s assistance on immigration enforcement.”

The footnote should be read as a warning sign, Stephen Vladeck, a law professor at Georgetown, wrote in a newsletter on Thursday. “The need to put in writing that dropping the prosecution was not in exchange for ‘assistance on immigration enforcement,’” he wrote, “sure seemed to strongly imply that actually … it was.”

Mr. Bove, in a sentence in some tension with Mr. Jackson’s speech, said the administration would soon turn its attention to a new target. “There is also questionable behavior reflected in certain of the prosecution team’s decisions,” he wrote, “which will be addressed in the forthcoming investigations.”