Geoffrey S. Berman, the chief federal prosecutor in New York, resigned after a remarkable standoff with Attorney General William Barr and contradictory comments from President Donald Trump.

Berman, who signaled he’d fight to keep his position to protect sensitive investigations being run by his office in Manhattan, said on Saturday evening that he would step down after Barr switched course on who would take over for him on an interim basis.

Berman will be replaced by Deputy U.S. Attorney Audrey Strauss, a trusted prosecutor in the office who had already been overseeing Trump-related investigations, Barr said. On Friday night, the attorney general said the interim role would be filled by Craig Carpenito, currently the U.S. attorney for New Jersey, but he backed off on that and appointed Strauss.

“In light of Attorney General Barr’s decision to respect the normal operation of law and have Deputy U.S. Attorney Audrey Strauss become Acting U.S. Attorney, I will be leaving the U.S. Attorney’s Office for the Southern District of New York, effective immediately,” Berman said in a statement.

“It is evident that Mr. Berman viewed a departure from that traditional succession as a threat to the Office’s cherished independence,” said John Zach, a former prosecutor in the office. “After the Justice Department relented and permitted his highly respected deputy to take over, he knew the ship was safe and was apparently satisfied that he had protected the office from potential outside interference.”

Berman called Strauss “is the smartest, most principled, and effective lawyer with whom I have ever had the privilege of working.”

‘Quite Disappointed’

In a letter to Berman on Saturday afternoon, Barr said he was disappointed that Berman hadn’t stepped aside willingly so the Justice Department could replace him with Jay Clayton, chairman of the U.S. Securities and Exchange Commission, following confirmation by the Senate.

“I was surprised and quite disappointed by the press statement you released last night,” Barr said, referencing Berman’s rebellious refusal late Friday night. “You have chosen public spectacle over public service.”

“To the extent that your statement reflects a misunderstanding concerning how you may be displaced, it is well-established that a court-appointed U.S. Attorney is subject to removal by the President.”

Trump, departing the White House on Saturday afternoon for a rally in Oklahoma, didn’t confirm he had taken any action on Berman.

“Attorney General Barr is working on that. That’s his department, not my department. But we have a very capable attorney general, so that’s really up to him. I’m not involved,” Trump told reporters.

Whither Clayton?

Consideration of a Clayton nomination by the Senate was also in question. Senate Judiciary Chairman Lindsey Graham indicated he won’t move forward without the consent of the state’s two senators, both Democrats, who have decried Berman’s removal. But Graham later endorsed Trump’s power to remove a political appointee, and praised Strauss.

Barr’s letter on Saturday also rejected Berman’s assertion that he needed to stay on the job to protect investigations that are currently underway by the office.

“This is obviously false,” Barr said. “I fully expect that the office will continue to handle all cases in the normal course and pursuant to the Department’s applicable standards, policies, and guidance.”

The Barr letter deepens the mystery about what discussions Barr and Berman had in the hours or days before Barr’s surprise statement announcing Berman’s purported resignation after 9 pm on Friday night. Berman issued his own statement after 11 pm saying he’d received no notice the announcement was coming and had no intention of resigning.

‘I Have Not Resigned’

“I learned in a press release from the Attorney General tonight that I was ‘stepping down’ as United States Attorney. I have not resigned,” Berman’s said in his Friday night statement. “Our investigations will move forward without delay or interruption. I cherish every day that I work with the men and women of this office to pursue justice without fear or favor -- and intend to ensure that this Office’s important cases continue unimpeded.”

The Manhattan U.S. attorney’s office is perhaps the nation’s most elite and storied law enforcement office, taking a leading role in prosecuting white-collar fraud on Wall Street, terrorist plots and attacks, political corruption and organized crime, among other things.

It cracked down on insider trading in the aftermath of the 2008-2009 financial crisis, eroded the influence of the mafia in New York, and prosecuted state and federal politicians for self-dealing. The office is fiercely independent, frequently referred to as the “Sovereign District of New York.”

Trickest Phase

But following the end of Robert Mueller’s investigation into Russian interference in the 2016 election, the New York office may have entered its trickiest phase, as the lead authority scrutinizing the conduct of the leader of the free world and his close associates.

Line prosecutors in the office were initially wary of Berman, who served as a volunteer for Trump’s presidential transition team and who was installed in the post on an interim basis and never confirmed by the Senate (he was confirmed by the judges of the New York federal court in alternative process).

But Berman, 60, has since won the admiration of prosecutors there for the work he’s overseen and his efforts to protect the office’s independence and integrity, especially amid ongoing chatter of political pressure from Washington.

In his ongoing investigation into the late Jeffrey Epstein’s sex crimes and those who enabled his behavior, Berman just this month publicly refuted a statement from Prince Andrew’s U.K. lawyers that he has repeatedly sought to talk to American investigators. In an extraordinary showdown, Berman issued his own statement that the prince has done nothing of the kind.

Since Trump took office, federal prosecutors in New York have pursued several investigations into the president, his companies, and people close to him. That includes the prosecution of Trump’s long-time onetime personal lawyer and “fixer” Michael Cohen, and a current investigation involving Trump ally Rudy Giuliani and efforts to secure political dirt in Ukraine on presidential rival Joe Biden.

Deutsche Bank

There has also been a long-running investigation into Deutsche Bank, a crucial financial backer of Trump’s companies. A forthcoming book by National Security Adviser John Bolton that’s dominated the news this week said Trump had previously sought to meddle with a case being pursued by the office.

Before Friday’s announcement, Barr had asked Berman to step aside and offered him other roles in the Justice Department, including head of the Civil Division at main Justice, said a Justice Department official familiar with the matter who asked not to be named. Berman declined, the person said.

Barr had in his earlier statement that Berman would leave office July 3, and that the Manhattan office would be led on an interim basis by Craig Carpenito, currently the U.S. attorney for New Jersey.

The dueling statements on Friday night stunned people in legal and political circles and raised questions about the move, including from Preet Bharara, Berman’s predecessor, whom Trump fired in 2017 after he refused to quit.

Jerrold Nadler, chairman of the House Judiciary Committee, which has oversight of the Justice Department and had a lead role in Trump’s impeachment, said on Twitter that he would invite Berman to testify at a hearing on June 24. Nadler is scheduled to appear on CNN on Sunday morning.

SDNY was pursuing several probes of the president’s business and his inaugural committee. As well as its investigation into Giuliani, it has charged two of Giuliani’s associates. In his congressional testimony, Cohen, whose conviction on campaign finance violations and other charges was secured by SDNY prosecutors, said he was cooperating with them on matters he couldn’t discuss.

In charging Cohen in late 2018, prosecutors said he acted at the direction of “Individual 1,” whom they didn’t identify. But Cohen later said that individual was Trump.

Trump and Erdogan

The office has charged Turkey’s state-owned Halkbank with helping Iran evade sanctions on billions of dollars in oil funds. The bank has pleaded not guilty. According to Bolton’s forthcoming book, Trump in 2018 told Turkey’s President Recep Tayyip Erdogan at a Group of 20 meeting that he thought Halkbank “was totally innocent of violating U.S. Iran sanctions.”

Bolton wrote that, “Trump then told Erdogan he would take care of things, explaining that the Southern District prosecutors were not his people, but were Obama people, a problem that would be fixed when they were replaced by his people.”

That appointment also raised questions for Dan Goldman, a former federal prosecutor from the U.S. attorney’s office in Manhattan who served as a House Intelligence Committee lawyer and grilled a dozen witnesses during the panel’s public impeachment hearings. He said on Twitter that what happened Friday wasn’t standard procedure.

According to a Justice Department official, Barr has known Clayton for years and holds him in high regard. Clayton was getting ready to leave the administration and go back to New York, the person said. He expressed interest in SDNY and the Attorney General thought it was a good idea, according to the official.

On enforcement matters at the SEC, Clayton, a political independent, has been willing to penalize firms accused of wrongdoing over Republican objections. During his tenure, the agency has also rewritten conduct standards for brokers and taken steps to clamp down on fees that stock exchanges charge. An SEC spokesperson for Clayton didn’t immediately respond to e-mailed messages seeking comment.