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Months of strain date back to the investigation into the former F.B.I. official Andrew McCabe and growing fears of political interference.
WASHINGTON — In the days before they filed the sentencing recommendation for President Trump’s friend Roger J. Stone Jr. that helped plunge the Justice Department into turmoil, the prosecutors on the case felt under siege.
A new boss, Timothy Shea, had just arrived and had told them on his first day that he wanted a more lenient recommendation for Mr. Stone, and he pushed back hard when they objected, according to two people briefed on the dispute. They grew suspicious that Mr. Shea was helping his longtime friend and boss, Attorney General William P. Barr, soften the sentencing request to please the president.
In an attempt to ease the strain, David Metcalf, Mr. Shea’s chief of staff, clasped his hand on the shoulder of one of the prosecutors, Aaron S.J. Zelinsky, as they passed in a hallway. But the gesture prompted a terse and sharp verbal exchange, according to three people briefed on the encounter. As word of the spat spread through the office, unfounded rumors swirled that the altercation had been physical.
Skepticism of Mr. Shea, the acting U.S. attorney for Washington, only deepened in his 600-person office when Mr. Barr quickly intervened to recommend a lighter sentence for Mr. Stone just as the president declared on Twitter that the government was treating his friend too harshly.
Within a day, Mr. Zelinsky and three others quit the case, one resigning from his job entirely. Their protest engulfed the Justice Department in turmoil that could damage its treasured reputation for political independence.
At the center of the crisis is the U.S. attorney’s office in Washington, one of the largest collections of federal prosecutors in the country. Over the decades it has handled some of the nation’s most sensitive cases, including the corruption scandal involving the prominent lobbyist Jack Abramoff and the conviction of the main suspect in the 2012 Benghazi, Libya, attacks.
The Washington office, which operates separately from the main Justice Department, took over the continuing cases last year from the special counsel, Robert S. Mueller III, after he closed his inquiry into Russia’s election interference. He found insufficient evidence to charge anyone tied to the Trump campaign with conspiring with Moscow but charged several Trump associates with other crimes, including Mr. Stone.
The tensions between the office, the Justice Department and the White House date back further than the tumult in the Stone case. They have been simmering since at least last summer, when the office’s investigation of Andrew G. McCabe, a former top F.B.I. official whom the president had long targeted, began to fall apart.
Mr. Shea’s predecessor, Jessie K. Liu, a lawyer whom Mr. Trump had appointed to lead the office in 2017, pressed the McCabe case even after one team of prosecutors concluded that they could not win a conviction. After a second team was brought in and also failed to deliver a grand jury indictment, Ms. Liu’s relationship with Mr. Barr grew strained, people close to them said. She left the position this year, though she and Mr. Barr have both stressed to associates that her departure was amicable.
Still, her exit unnerved prosecutors and set off the chain of events that culminated in the current crisis, in which prosecutors in the office began to worry that Mr. Barr was intervening in sensitive cases for political reasons even as he has publicly pushed back against Mr. Trump, a rebuke the president has ignored.
Mr. Barr has denied any political motivations. But as Mr. Shea took over, the attorney general assigned outside prosecutors to re-examine politically fraught cases, including that of Michael T. Flynn, Mr. Trump’s former national security adviser.
The string of events “suggests undue meddling by higher-ups at the Justice Department or elsewhere,” said Channing Phillips, an acting U.S. attorney in Washington under President Barack Obama.
A Justice Department spokeswoman declined to comment for this article, which is based on interviews with nearly a dozen current and former department lawyers who have worked with the U.S. attorney’s office in Washington and others familiar with their work.
In a statement in response to questions about tensions in the office and whether he would stay, Mr. Shea said he had prepared “my whole life” for the post and called it “the ultimate job in federal law enforcement.”
He added, “You can impact people’s lives in a very meaningful way by protecting them from violent crime, hate and terrorism.”
When Mr. Shea took over on Feb. 3, he knew he had inherited a series of political land mines. What he did not appear to realize was how mistrustful many of the federal prosecutors in Washington had become of the main Justice Department, and of Mr. Barr.
Their misgivings ramped up last summer, as Ms. Liu worked with prosecutors to investigate whether Mr. McCabe had lied to investigators during an administrative inquiry.
Prosecutors liked Ms. Liu in part because they felt she shielded them from political pressures, even as Mr. Trump publicly accused Mr. McCabe on Twitter of lying and misconduct. And she had a reputation for being a good soldier who had stayed on even as she was passed over for top Justice Department posts.
The McCabe case had always been politically charged: Investigators were scrutinizing an accomplished former top law enforcement official whom the president had repeatedly attacked for his deep involvement in the Russia investigation. The inquiry focused on whether he misled internal investigators examining the source of disclosures of sensitive information in a Wall Street Journal article.
But the case eventually fell apart because a number of hurdles proved too steep, including problematic witnesses and prosecutors’ concerns that Mr. Barr’s handling of the special counsel report would make their case look politicized, people familiar with the investigation said.
The two main prosecutors, Kamil Shields and David Kent, also came to believe that they could not get a jury to convict Mr. McCabe, the people said. They concluded that Mr. Trump’s relentless broadsides against Mr. McCabe had poisoned any potential jury, and they were worried about the appearance of a vindictive prosecution: Mr. McCabe revealed in early 2019 that he had opened the inquiry into whether Mr. Trump obstructed justice by firing James B. Comey as F.B.I. director.
Ms. Shields eventually left the case and the department. Mr. Kent also decided to quit the case. Two other prosecutors known for their aggressiveness, Molly Gaston and J.P. Cooney, took over.
An indictment seemed imminent after Ms. Liu and the deputy attorney general, Jeffrey A. Rosen, rejected pleas in September from Mr. McCabe’s lawyers to drop the investigation. The grand jury hearing the case was reconvened after months of inactivity, but the prosecution never appeared to advance.
The investigators’ difficulties began to creep into view in news reports, creating an awkward situation for Ms. Liu.
For months, her office refused to tell Mr. McCabe’s lawyers what was happening with the case. Informing a defense team eager to publicly clear its client would have almost certainly provoked the president’s anger, people close to Mr. McCabe speculated.
While the case remained in limbo, Ms. Liu had difficult conversations about it with officials at the main Justice Department, according to two people briefed on their discussions.
Ms. Liu sought a top Treasury Department job, and Mr. Barr made no attempt to stop her, according to three people briefed on her job search. A new role outside the Justice Department seemed to put to rest political issues for both her and Mr. Barr. Ms. Liu said she took the Treasury job only because she saw it as a good opportunity, people close to her said.
But Ms. Liu’s departure created unrest within her office.
She had initially emailed her office to say that she would remain in place until the Senate confirmed her to her new post, as is typical. But Mr. Barr then asked her to leave early in the new year, saying he was concerned he would have trouble finding a replacement if her confirmation process stretched on toward the end of Mr. Trump’s first term. Though Ms. Liu was taken aback, she eventually agreed to the terms but told few people in the U.S. attorney’s office.
By mid-January, administration officials found an assignment for her at the Treasury Department to take on while she awaited confirmation, and she sent an officewide email saying she would leave earlier than planned. Some of the prosecutors and other employees in the U.S. attorney’s office viewed the announcement and her departure just two weeks later as an abrupt end to her tenure and said they feared she was ousted because she failed to deliver on a prosecution that Mr. Trump openly sought.
Mr. Shea, who comes from a family of law enforcement officers, took over the office in early February, aware that Mr. Barr and the Justice Department had been parrying demands from the president to prosecute his enemies.
But according to two people who have spoken with Mr. Shea, he did not know that some prosecutors now working for him had come to view Mr. Barr not as their chief defender from political interference but as an agent of the president’s pressure campaigns on law enforcement.
Within days of Mr. Shea’s arrival, the Stone sentencing brought tensions to a head. When Mr. Barr sent word to the trial team that he wanted less than the seven to nine years outlined in federal sentencing guidelines that they planned to recommend, the lawyers viewed the directive as a last-minute order with no legal basis.
They expressed frustration that they had so little time to react, according to a person who heard their complaints; most of the team’s disagreement with Mr. Shea played out through intermediaries in the office.
Ultimately, they threatened to withdraw from the case if they were pressured to file a recommendation to the judge that they disagreed with.
Mr. Shea was caught off guard. Even though he agreed with Mr. Barr that following the guidelines allowed for too harsh of a punishment recommendation, he told associates he could not afford to alienate the Stone trial team as his first act on the job.
On the day that the filing was due, Mr. Shea told the attorney general that the prosecutors planned to stick to their recommendation but that “he thought that there was a way of satisfying everybody and providing more flexibility,” Mr. Barr said in an interview with ABC News.
Mr. Barr was left with the misimpression that the team would lay out the factors for Judge Amy Berman Jackson to weigh under the federal guidelines but ask for a lesser sentence. Their filing proved otherwise.
Mr. Barr told ABC that he immediately asked that prosecutors replace it with a more lenient request. But coming alongside the president’s middle-of-the-night protest on Twitter, it created the appearance that the attorney general was heeding political pressure.
The tensions between the U.S. attorney’s office and senior Justice Department leaders exploded into the open. The four prosecutors who withdrew from the Stone prosecution left behind more than a year’s worth of work in the final stages of the case. The chaos crushed morale in the U.S. attorney’s office, according to eight current and former Justice Department employees. Federal prosecutors around the country began to privately articulate fears of political interference.
Mr. Barr moved quickly to blunt the turmoil. He declared in the ABC interview that the president’s tweets were making it “impossible” to do his job, an unusually public rebuke.
Mr. Shea also sought to calm his office. “While there are times where reasonable minds may disagree, I respect the work that each of you do, and I will do my best to support our work,” he wrote in an email to the staff on the evening after the prosecutors withdrew from the Stone case.
Judge Jackson sentenced Mr. Stone last week to more than three years in prison, challenging one of the case’s new prosecutors about the recent disarray. He apologized, but also caused more confusion when he defended the argument for a stiff sentence without disavowing the request for a lighter punishment.
Still, officials at both the U.S. attorney’s office in Washington and the Justice Department expressed hope that the sentencing would help hasten a return to calm in both buildings. Mr. Shea has spent the past two weeks on a listening tour of his office, meeting with hundreds of lawyers.
Whether the storm has passed remains to be seen. The reviews of the Flynn case and others are continuing. And hours after Mr. Stone was sentenced, the president called again for his exoneration.
Charlie Savage contributed reporting.
