On Wednesday afternoon, the highest ranking federal prosecutor in Manhattan, Jay Clayton, was blindsided.
He had just learned that officials in Washington had decided to fire Maurene Comey, a veteran prosecutor in his office, without first notifying him, according to three people with knowledge of the interaction. He was not told the reason.
The sudden firing from the Southern District of New York — and Mr. Clayton’s inability to intervene — raised questions about his autonomy as the leader of an office that has long prided itself on its independence from Washington and has led high-profile investigations into public corruption, financial crimes and gang violence.
The episode typified the chaos that has gripped four U.S. attorney’s offices in the New York region since President Trump reclaimed the White House, taking closer control of the Justice Department than any president in the last half-century and rattling the nation’s legal system.
None of the offices in Manhattan, Brooklyn, Albany and Newark has a permanent leader. Instead, Mr. Trump has concentrated power within the Justice Department in Washington and, in two of the offices, has elevated loyalists with little prosecutorial experience, leading to confusion and plummeting morale within the rank and file.
His moves raise the question of what, exactly, a U.S. attorney is empowered to do, beyond serving Mr. Trump’s chosen agenda.
“It’s not a one-off,” said Daniel Richman, a professor at Columbia Law School and a former federal prosecutor in Manhattan. “Sad to say, there are a number of U.S. attorney’s offices across the country that have been caught in various partisan efforts that have reduced the quality of the work they do, and the respect they get.”
Though U.S. attorney’s offices have always answered to top Justice Department officials in Washington, they have historically enjoyed a certain sway over their own territory, including the ability to hire and fire and to conduct investigations without micromanagement from the Washington headquarters, typically referred to as Main Justice.
The Southern District in particular has historically set its own course, earning the nickname the Sovereign District. But on Wednesday, Mr. Clayton was reduced to a bystander.
“The role of the U.S. attorney is to mediate between the dictates from Washington and the integrity of the office’s day-to-day work,” Professor Richman said. “And if he can’t do that, he’s just a paper-pusher.”
A spokesman for the Southern District declined to comment.
The ouster of Ms. Comey, who is the daughter of James B. Comey, the former F.B.I. director and an adversary of President Trump, was just the latest jolt to the Southern District in Mr. Trump’s second term. In February, the administration moved to drop corruption charges against Mayor Eric Adams of New York City, saying they were hindering him from helping with immigration enforcement. The office’s interim U.S. attorney, Danielle R. Sassoon, resigned in protest.
She was succeeded by an interim official who held the office for about two months before Mr. Trump named Mr. Clayton, who served as chairman of the Securities and Exchange Commission during Mr. Trump’s first term. But Mr. Clayton, like the U.S. attorneys in Newark, Brooklyn and Albany, remains unconfirmed by the Senate.
Senator Chuck Schumer of New York, a Democrat, used a Senate provision known as a blue slip to block the nominations of Mr. Clayton and Joseph Nocella Jr., the interim U.S. attorney in Brooklyn. That has left it unclear how long they can continue to lead those storied New York offices. Mr. Clayton’s 120-day term expires in mid-August. After that, if he remains unconfirmed, the judges of the federal court in the Southern District could appoint him.
In Mr. Trump’s first term, all 85 of his nominees for U.S. attorney were confirmed by the Senate. But so far in his second term, he has formally nominated only around a quarter of that figure, relying on interim and acting officials to lead offices around the country.
Of the four U.S. attorneys in the New York region, the tenure of John A. Sarcone III, Mr. Trump’s choice to lead the U.S. attorney’s office in Albany, has perhaps been marked by the most personal disarray. Mr. Sarcone, who took over in March as head of the office, was never formally nominated to lead it.
Mr. Sarcone had never worked as a prosecutor before his elevation, and had been a regional administrator for the General Services Administration, which manages the federal government’s property portfolio. In his brief tenure, Mr. Sarcone has harshly criticized immigrants and the Albany police and removed The Albany Times Union from his office’s press distribution lists for its probing coverage of his leadership.
This week, still lacking Senate confirmation, Mr. Sarcone needed the approval of the judges of the Northern District of New York in order to extend his tenure. But in a rare decision, the judges declined to appoint him as the office’s permanent leader. After that, Mr. Sarcone was reappointed by the Justice Department to lead the office as a “special attorney to the attorney general.”
A spokesman for the U.S. attorney’s office in Albany declined to comment.
In New Jersey, Alina Habba, Mr. Trump’s former campaign spokeswoman and personal lawyer, has courted controversy as the interim U.S. attorney. She has aggressively targeted critics of the Trump administration, including by investigating and bringing charges against Democratic elected officials.
In May, a magistrate judge in New Jersey admonished her office’s prosecutors during a hearing in which the prosecutors dropped trespassing charges against Ras Baraka, the mayor of Newark.
Ms. Habba, who was also appointed in March and had no prior prosecutorial experience, previously ran a small civil litigation firm. She met Mr. Trump through his Bedminster, N.J., golf club, and started working for him in 2021.
Like Mr. Sarcone, Ms. Habba faces a deadline to be named permanent U.S. attorney for the District of New Jersey, and may face challenges to a court appointment. On Thursday, she acknowledged as much in an all-hands meeting at her office, thanking prosecutors for their work should she not be voted in.
In Brooklyn, President Trump has appointed Mr. Nocella, a former Long Island family court judge and a product of Long Island Republican politics. Mr. Nocella is the only one of the four who had any experience as a federal prosecutor before being appointed, having served as an assistant U.S. attorney in the Eastern District of New York in the early 1990s.
That office, which has been a leader in cases prosecuting the leaders of drug cartels, transnational repression by the Chinese government and public corruption, has experienced less turmoil than its counterparts in Manhattan, Albany and Newark.
A spokesman for the Eastern District declined to comment. The U.S. attorney’s office in New Jersey did not respond to a request for comment.
The deputy attorney general, Todd Blanche, a former federal prosecutor in Manhattan, has emphasized the particular importance of the Brooklyn office to Mr. Trump — in part because it includes Kennedy Airport, a nexus for international criminal cases, according to two people with knowledge of his thinking. Mr. Blanche has also emphasized the importance of relying on the expertise and experience of veteran prosecutors in the office to help execute the president’s law-and-order agenda, the people said.
But the Brooklyn office also hasn’t been entirely insulated. In March, before Mr. Nocella was appointed, some members of the office were stunned when they learned that Carlos Watson, the convicted fraudster, had been granted clemency by President Trump, according to two people with knowledge of the situation.
“The message seems to be that unitary executive gets to do what it wants, and damn those who interfere,” Mr. Richman said.
Santul Nerkar is a Times reporter covering federal courts in Brooklyn.
Jonah E. Bromwich covers criminal justice in the New York region for The Times. He is focused on political influence and its effect on the rule of law in the area’s federal and state courts.
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