WASHINGTON — While Attorney General William Barr asserted his independence from the White House this week, he has also been quietly intervening in a series of politically charged cases, including against Michael Flynn, President Donald Trump’s former national security adviser, people familiar with the matter said Friday.

Barr installed a phalanx of outside lawyers to reexamine national security cases with the possibility of overruling career prosecutors, a highly unusual move that could prompt more accusations of Justice Department politicization. The case against Flynn, who twice pleaded guilty to lying to the FBI in the Russia investigation, is a cause célèbre for Trump and his supporters, who say the retired general was ensnared in a “deep state” plot against the president.

The disclosures came as Trump made clear Friday that he believes he has free rein over the Justice Department and its cases, rejecting Barr’s public demand of a day earlier that the president stop commenting on such cases.

Citing Barr’s assertion in an interview Thursday that Trump had never asked him to act in a criminal case, the president declared on Twitter: “This doesn’t mean that I do not have, as President, the legal right to do so, I do, but I have so far chosen not to!”

Hours later, the Justice Department told defense lawyers for Andrew McCabe, the former acting FBI director who Trump has vilified for his role in the Russia case, that McCabe would not be charged in connection with a leak case, ending a nearly two-year criminal investigation.

“We consider the matter closed,” the department wrote to McCabe’s lawyers.

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Together, the developments send conflicting signals at a time when the Justice Department’s independence from political interference by the White House has come under sharp scrutiny.

Barr publicly challenged Trump after the turmoil this week over the case against Roger Stone, Trump’s longtime friend and political adviser, threatened to erupt into a full-blown crisis.

After prosecutors recommended Monday a seven- to nine-year sentence for Stone on seven felony convictions, the president criticized the move. Senior law enforcement officials overruled the career prosecutors the next day, immediately prompting accusations of political interference.

Though Barr said that he had intended to intervene to ask a judge to impose a more lenient sentence, he also said that Trump had complicated his plans by creating the specter of political tampering and that the president’s commentary was making his job “impossible.”

The four prosecutors involved in the case out of the U.S. Attorney’s Office in Washington quit it.

Stone’s lawyers filed a sealed motion Friday seeking a new trial, which could delay his sentencing scheduled for next week. It came a day after Trump alleged juror bias in Stone’s trial.

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Barr installed the outside lawyers at the start of February and put them in a position to second-guess decisions on those cases, people familiar with the office’s workings said. Among the outsiders were Jeff Jensen, who Trump appointed as the U.S. attorney in St. Louis in 2017, and aides to Jeffrey A. Rosen, the deputy attorney general.

Barr’s intervention was described by multiple people who spoke on the condition of anonymity to discuss the delicate internal deliberations. The Justice Department declined to comment.

The attorney general has also recently installed a personal aide, Timothy Shea, as interim U.S. attorney in Washington. Barr had previously maneuvered to get the former U.S. attorney there, Jessie K. Liu, to leave her position earlier than she had planned, creating a vacancy.

The outside officials have begun grilling line prosecutors in the Washington office about various cases — some of which are publicly known, and some of which are not — including investigative steps, prosecutorial actions and why they took them, according to the people.

Among the most politically charged is the case against Flynn, which Jensen is said to now be overseeing. Flynn’s case had been developed during the Russia investigation by the office of the special counsel, Robert Mueller, and was handed off to the U.S. Attorney’s Office in Washington after Mueller completed his investigation.

Flynn’s defense lawyers, led by Sidney Powell, had urged Barr to intervene in the case, accusing the special counsel’s prosecutors of being corrupt. In June, shortly before she officially became Flynn’s lawyer, Powell wrote to Barr to suggest that new prosecutors review the case, expressing her “fervent hope that you and the Department of Justice will use this case to restore integrity and trust in the department.”

Though the president fired Flynn, Trump has long derided the case against him, wishing him luck on Twitter, praising Powell and calling the case a “disgrace.”

Powell has hurled waves of unsubstantiated charges of prosecutorial misconduct, hoping to derail the case against her client. The judge in the case, Emmet G. Sullivan, rejected them and refused to hold prosecutors in contempt as Powell demanded, later prompting Flynn to seek to withdraw his guilty plea. In the latest salvo, prosecutors again slapped down Powell’s accusations of government malfeasance.

“The defendant relies on allegations that do not pertain to his case, that the court already rejected, and that have no relevance to his false statements to the FBI,” prosecutors wrote in a filing Wednesday.

That filing provided no public indication that Jensen was playing a role behind the scenes in the case, or whether he had reviewed its text and permitted the prosecutors to file it.

Prosecutors had initially sought zero to six months in prison for Flynn, then softened their tone and said they would not oppose the lowest end of that range — probation instead of prison. That shift came in late January, before the change in the Washington office’s leadership.

Amid the heightened scrutiny of the Justice Department, the timing of officials’ decision to end their long-running investigation into McCabe without charges was striking.

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Prosecutors in the Washington office told McCabe’s lawyers of their decision Friday morning, the lawyers, Michael R. Bromwich and David Schertler, said in a statement.

“We said at the outset of the criminal investigation, almost two years ago, that if the facts and the law determined the result, no charges would be brought,” they said. “We are pleased that Andrew McCabe and his family can go on with their lives without this cloud hanging over them.”

McCabe’s case centered on whether he made a false statement to the department’s inspector general about a disclosure to reporters regarding an investigation into the Clinton Foundation. McCabe, working through the FBI press office, had authorized a spokesman and a bureau lawyer to speak to a reporter to rebut allegations that he had slowed the inquiry, when in fact he had pushed to protect it.

McCabe’s lawyers had denied that he intentionally lied to the inspector general investigators. In September, Justice Department officials told McCabe’s lawyers that they had rejected a last-ditch appeal to not charge him. Why the case lingered for months without a decision is unclear.

Also Friday, Judge Reggie B. Walton of U.S. District Court for the District of Columbia, who is presiding over a lawsuit seeking FBI documents related to McCabe’s firing in 2018, unsealed the transcript of a September closed-door meeting with prosecutors.

Noting that prosecutors had said weeks earlier that a decision about charging McCabe could come “literally within days,” Walton chastised them for stringing along McCabe and noted Trump’s comments about McCabe with disapproval, saying they created the appearance of a “banana republic.”

“I don’t think people like the fact that you got somebody at the top basically trying to dictate whether somebody should be prosecuted,” the judge said, adding that even if Trump’s moves are “not influencing the ultimate decision, I think there are a lot of people on the outside who perceive that there is undo, inappropriate pressure being brought to bear.”