The former Russian diplomat faced several charges, including money laundering, that could have landed him behind bars for a long time. But in June, shortly before his trial, the Manhattan U.S. attorney’s office accepted a guilty plea from the man to only one charge, which might let him avoid prison altogether.
The judge, Jed S. Rakoff, said he was curious: Was the office’s change in position discussed with or initiated by the Justice Department in Washington?
“No, your honor,” a prosecutor replied.
“OK,” Judge Rakoff said. “I wanted to make sure we didn’t have an Adams situation here.”
The judge was referring to the resignation in February of the head of the U.S. attorney’s office after she refused a Trump Justice Department edict to seek the dismissal of charges against New York’s mayor, Eric Adams. The department then orchestrated the dismissal anyway.
The former diplomat’s guilty plea proceeded as planned, but the courtroom exchange was revealing. It showed that judges still have lingering concerns about the independence and authority of the U.S. attorney’s office for the Southern District of New York, now led on an interim basis by Jay Clayton, President Trump’s pick to be the top prosecutor.
The issue is expected to crystallize later this month when the roughly four dozen judges of the Southern District court, based in Manhattan, are to vote on whether to appoint Mr. Clayton to remain in the post.
President Trump originally nominated Mr. Clayton in January to serve as the U.S. attorney. But in April, after New York’s senior Democratic senator, Chuck Schumer, used a senatorial courtesy to block the confirmation of Mr. Clayton, the president appointed him on an interim basis.
With his 120-day interim term expiring later this month, the judges could choose to appoint Mr. Clayton or someone else to fill the vacancy until a Senate-confirmed U.S. attorney can take office.
In recent months, independent institutions like law firms and universities have faced demands by the Trump administration for policy changes and large financial payments by negotiating settlements or pushing back through litigation. Judges, too, have confronted Mr. Trump, both inside courtrooms and also over his choices to run U.S. attorney’s offices.
In New Jersey and upstate New York, after federal judges refused to continue the terms of interim U.S. attorneys named by Mr. Trump, the administration moved to keep the president’s choices in their posts.
Mr. Trump had named Alina Habba, his former lawyer, as interim U.S. attorney for New Jersey. With her term expiring last month, the judges filled the position with Desiree L. Grace, an experienced federal prosecutor in the office, rather than Ms. Habba.
Justice Department officials then fired Ms. Grace, with Attorney General Pam Bondi declaring in a social media post, “This Department of Justice does not tolerate rogue judges.”
In Albany, N.Y., after judges refused to keep John A. Sarcone III as head of the office there, the administration gave him the title “special attorney to the attorney general” and made him the acting U.S. attorney for the Northern District of New York.
Mr. Clayton, although never a prosecutor, was a longtime corporate lawyer at the firm Sullivan & Cromwell and served as chairman of the Securities and Exchange Commission during Mr. Trump’s first term. As the interim U.S. attorney for the Southern District of New York, he named former veteran prosecutors from that office to serve as his deputy and as head of its criminal division.
The dismissal of the Adams case preceded Mr. Clayton’s tenure. But he came under criticism last month when the Trump administration fired Maurene Comey, a career federal prosecutor in his office who had worked on the sex-trafficking cases of Jeffrey Epstein and his companion, Ghislaine Maxwell. Ms. Comey was one of the prosecutors who tried, and obtained the conviction of, Ms. Maxwell, who is serving a 20-year prison sentence.
Ms. Comey is also the daughter of James B. Comey, the former F.B.I. director and a critic of Mr. Trump. Mr. Comey was fired by Mr. Trump during his first term.
The New York Times has reported that Mr. Clayton was blindsided by Ms. Comey’s dismissal, which occurred without explanation, and he has not publicly commented on the episode. A spokesman for Mr. Clayton declined to comment for this article.
Legal experts who closely follow the Southern District are debating whether Ms. Comey’s firing — and recent chaos surrounding the prosecutor appointments elsewhere — will affect the judges’ vote on Mr. Clayton.
“I would assume that the judges are asking themselves, ‘Jay Clayton, as compared to what?’” Rachel E. Barkow, a law professor at New York University, said. “I think the ‘as compared to what’ question shows there are really scary alternatives out there.”
The judges of the Southern District are deeply familiar with the U.S. attorney’s office, whose prosecutors appear regularly before them and who, in many cases, worked for the judges as law clerks. And more than a third of the judges listed on the court’s website had once worked in the office before joining the bench.
Not surprisingly, the debate over Mr. Clayton and what the court will decide has extended to the office’s alumni.
Daniel C. Richman, a former federal prosecutor for the office who now teaches criminal law at Columbia, said he expected the judges to ultimately pick Mr. Clayton.
“We’re now seeing the consequences of refusal to accept the administration’s choice,” Professor Richman said. “I mean aggressive pushback by the president and the attorney general, in the form of hiring either the same people or worse people.”
“I don’t think the judges are looking to pick a fight for no good reason,” Professor Richman added.
Jessica A. Roth, who teaches criminal law at the Benjamin N. Cardozo School of Law, said the events surrounding the Comey firing “without cause or any process raise significant concerns about the office’s independence under his watch.”
“In making their choice,” she said, “the judges will seek to appoint an individual who is professionally qualified for the role and who will protect the office from political interference.”
Two former prosecutors, writing in The Contrarian, criticized Mr. Clayton for his public silence on Ms. Comey’s firing. They also faulted the Justice Department for having the deputy attorney general interview Ms. Maxwell, as opposed to “the prosecutor’s office that convicted Maxwell and has the most knowledge of her crimes.”
That Mr. Clayton “has not publicly defended Comey and S.D.N.Y.’s handling of Epstein shows he likely has been cowed into submission by this administration,” the former prosecutors, Mimi Rocah and Jacqueline Kelly, wrote.
Steven R. Peikin, a former prosecutor who later worked as the S.E.C.’s chief of enforcement under Mr. Clayton and was a partner with him at Sullivan & Cromwell, called him a principled leader.
“In any important job you deal with a lot of difficult situations that raise significant issues — legal and ethical and professional and personal,” Mr. Peikin said, “and I never saw Jay do anything that I didn’t respect and admire.”
Sarah Krissoff, a former prosecutor and now defense lawyer, said she believed that although Mr. Clayton lacked a prosecutor’s experience, his tenure leading the S.E.C. gives him the kind of bona fides “that’s going to be important to the judges.”
John S. Martin Jr., who served as U.S. attorney and later as a federal judge, both in the Southern District, said he would have resigned if an administration had fired one of his top career prosecutors.
But Mr. Martin added that he was unsure whether that was a reason for the court not to appoint Mr. Clayton.
“I don’t know the factors that went into his decision not to quit,” he said. “There may be a lot of other things that they’ve tried to do that he’s been able to block, and the best thing for the office is for him to stay.”