WASHINGTON — The U.S. attorney who had presided over an inconclusive criminal investigation into former acting FBI director Andrew McCabe was abruptly removed from that job last month in one of several recent moves by Attorney General William Barr to take control of legal matters of personal interest to President Donald Trump, according to multiple people familiar with the matter.

A person familiar with the matter has confirmed to NBC News that President Trump has now rescinded the nomination of the U.S. attorney, Jessie Liu, for a job as an undersecretary at the Treasury Department.

Liu also supervised the case against Trump associate Roger Stone. On Tuesday, all four line prosecutors withdrew from that case — and one quit the Justice Department altogether — after Barr and his top aides intervened to reverse a stiff sentencing recommendation of up to nine years in prison that the line prosecutors had filed with the court Monday. (Liu left before the sentencing recommendation was made.)

But that wasn’t the first time senior political appointees reached into a case involving a former Trump aide, officials told NBC News. Senior officials at the Justice Department also intervened last month to help change the government’s sentencing recommendation for Trump’s former national security adviser, Michael Flynn, who pled guilty to lying to the FBI. While once the prosecutors in the case had recommended up to six months in jail for Flynn, their latest filing now says they believe probation would be appropriate.

The new filing came on the same day Liu was removed from her job, to be replaced the next day by a former prosecutor selected by Barr. Liu had been overseeing the criminal investigation into McCabe, who was accused by the department’s inspector general of lying to investigators. McCabe has not been charged, despite calls by President Trump for him to go to prison.

The resignations and the unusual moves by Barr come as Trump has sought revenge against government officials who testified after being subpoenaed by congressional Democrats in their impeachment investigation. In the days since the Senate acquitted him, Trump fired his ambassador to the European Union, a political supporter the president nominated, and had other officials moved out of the White House.

“This signals to me that there has been a political infestation,” NBC News legal analyst Chuck Rosenberg, a former U.S. attorney, said on MSNBC. “And that is the single most dangerous thing that you can do to the Department of Justice.”

In the Stone case, a new filing Tuesday says the previous recommendation does not accurately reflect the Department of Justice’s position on what would be a reasonable sentence in this matter.” A nine year sentence “could be considered excessive and unwarranted under the circumstances,” the filing says, declining to recommend a specific term and instead asking the judge considers an “appropriate” sentence.

“I’ve never seen this happen, ever,” said Gregory Brower, a former U.S. attorney and senior FBI official. “I’d be shocked if the judge didn’t order the U.S. attorney to come into court to explain it.”

The interim U.S. attorney for Washington, Timothy Shea, was named by Barr on Jan. 30. His announcement noted it’s the largest U.S. attorney’s office in the country and highlighted Shea’s “reputation as a fair prosecutor.”

It didn’t mention that Liu had been unceremoniously pushed out. Liu had been picked for a job in the Treasury Department, and normally she would have remained as U.S. Attorney until the Senate voted on her nomination, current and former officials said. Trump has now rescinded her nomination as undersecretary for terrorism and financial crimes.

The revocation of the nomination was first reported by Axios.

The change in the Flynn sentencing recommendation, coming in the midst of the Trump impeachment trial, received less attention than it might have.

On Jan. 7, after Flynn moved to withdraw his guilty plea, prosecutors in the case recommended a sentence that included possible jail time. Their original recommendation was probation, given that Flynn had cooperated in special counsel Robert Mueller’s Russia investigation.

But, people familiar with the matter said, senior Justice Department officials pressured prosecutors to reverse course. On Jan. 29, the government filed a new document with the court saying a sentence of probation was “reasonable.”

The next day, Barr announced the appointment of Shea, a former federal prosecutor.

The announcement Tuesday that the government would seek a lighter sentence for Stone came just hours after Trump called the recommendation that Stone serve seven to nine years in jail “horrible and very unfair.”

“Cannot allow this miscarriage of justice!” he wrote on Twitter.

DOJ spokeswoman Kerri Kupec told NBC News that Barr had no contact with the White House, and that the decision to change the sentencing recommendation was made before the Trump tweet.

That has not stopped critics from questioning a decision by Barr to step into a case involving a longtime friend of Trump who was convicted of lying to Congress for the express purpose, prosecutors made clear at the trial, of protecting the president.

David Laufman, the Justice Department’s former counterintelligence chief, on Twitter called it “a shocking, cram-down political intervention in the criminal justice process. We are now truly at a break-glass-in-case-of-fire moment for the Justice Dept.”

“The narrative that’s been developing for a long time now is that all of these prosecutions of people connected to the president are the product of a hoax or a witch hunt,” Brower said. “The president appears to be acting on that belief.”