WASHINGTON — Attorney General William P. Barr testified before Congress last spring that “it’s time for everybody to move on” from the special counsel investigation into whether Trump associates conspired with Russia’s 2016 election interference.
Nearly a year later, however, it is clear that Mr. Barr has not moved on from the investigation at all. Rather, he increasingly appears to be chiseling away at it.
The attorney general’s handling of the results of the Russia inquiry came under fire when a federal judge questioned this week whether Mr. Barr had sought to create a “one-sided narrative” clearing Mr. Trump of misconduct. The judge said Mr. Barr displayed a “lack of candor” in remarks that helped shape the public view of the special counsel’s report before it was released in April.
In fact, Mr. Barr’s comments then were but the first in a series of actions in which he cast doubt not just on the findings of the inquiry by the special counsel, Robert S. Mueller III, and some of the resulting prosecutions, but on its very premise. In the process, Mr. Barr demoralized some of the department’s rank and file and lent credence to Republican politicians who seek to elevate the Mueller investigation into an election-year political issue — including Mr. Trump.
“I’m deeply troubled by what I’ve been seeing with Barr’s stewardship of the Justice Department,” said Nancy V. Baker, a scholar of attorneys general who studied Mr. Barr’s first stint in the post under President George Bush in the early 1990s. At the very least, she said, he has created the appearance that he does not “respect the longstanding norms of departmental independence.”
Some of Mr. Barr’s defenders insist that he is suffering from a situation beyond his control: namely, a president whose running commentary on criminal cases he has an interest in has sowed suspicion about the attorney general’s motives. In a ruling on Thursday in a Freedom of Information Act case over the Mueller report, Judge Reggie B. Walton of the United States District for the District of Columbia questioned whether Mr. Barr had redacted portions of the Mueller report in order to protect the president.
The department’s spokeswoman, Kerri Kupec, said on Friday that “the court’s assertions were contrary to the facts” and that Mr. Mueller’s team helped the attorney general decide what information should be kept out of public view.
Nonetheless, the judge’s criticism reinforced the impression that Mr. Barr has been on a mission to undercut the Mueller inquiry. In ever stronger terms, Mr. Barr has implied that Mr. Mueller was appointed in 2017 only because F.B.I. officials rushed without reason to escalate their suspicions about the Trump campaign into a full-blown investigation.
The Justice Department’s own inspector general rejected that premise late last year, finding that the bureau’s decision was justified by the facts. But Mr. Barr has assigned a federal prosecutor to investigate the matter further and has suggested that the inquiry might conclude that the F.B.I. acted in bad faith. Investigators are also said to be examining the intelligence agencies’ assessment that President Vladimir V. Putin of Russia interfered in the American presidential race on behalf of Mr. Trump.
Last month, Mr. Barr appointed another outside prosecutor to review a case that Mr. Mueller brought against the president’s former national security adviser Michael T. Flynn for lying to the F.B.I. And in a second case that the Mueller team brought against Roger J. Stone Jr., Mr. Trump’s longtime friend, the attorney general overruled career prosecutors to seek a more lenient prison sentence, triggering a chain of events that the federal judge overseeing the case called “unprecedented.”
In those and other instances, Mr. Barr has never mentioned Mr. Mueller by name. But he has increasingly sided with the view of Mr. Trump and his allies that the special counsel’s inquiry was baseless. As Mr. Barr put it succinctly in a December interview with NBC News, “Our nation was turned on its head for three years, I think, based on a completely bogus narrative.”
He has implicitly criticized both John O. Brennan, the C.I.A. director under President Barack Obama, and James B. Comey, whom Mr. Trump fired as F.B.I. director in 2017, for actions related to the Russia inquiry. Noting that Mr. Brennan twice warned the Russian government not to interfere in the 2016 election, Mr. Barr said it was “inexplicable” no one warned the Trump campaign that the Russians had targeted it.
He also said Mr. Comey refused to take the necessary security clearance steps that would have enabled him to cooperate fully with Michael E. Horowitz, the department’s inspector general, in his review of aspects of the Russia investigation. But he noted that John H. Durham, the United States attorney for Connecticut who is separately investigating the origins of the Russia inquiry, has the power to compel testimony. “A decision has to be made about motivations,” he said.
The president’s allies are eager to draw Mr. Barr more publicly to their side. At an expected upcoming oversight hearing of the Senate Judiciary Committee, Senate Lindsey Graham, the Republican of South Carolina who chairs the panel, is likely to question Mr. Barr about whether he believes the Mueller inquiry was necessary or justified.
Representative Devin Nunes, Republican of California and another staunch defender of the president, has promised to ask the Justice Department to open a criminal inquiry into whether the special counsel’s office mishandled the prosecution of George Papadopoulos, a former Trump campaign adviser who pleaded guilty to lying to the F.B.I.
Both Mr. Barr’s critics and defenders are carefully watching the Flynn case for signs that Mr. Barr is backing away from what had been an aggressive prosecution initiated by Mr. Mueller and inherited by the United States attorney’s office in Washington. More than two years after he pleaded guilty and agreed to cooperate with the government, Mr. Flynn reversed himself and asked to withdraw his plea. He claimed prosecutors had deceived him — accusations that the judge overseeing the case has firmly rejected.
Once Mr. Flynn recanted, prosecutors stiffened their sentencing recommendation, saying Mr. Flynn deserved up to six months in prison. But in January, they seemed to soften that stance, saying that probation was also “reasonable.”
Outside prosecutors have now been assigned to review the Flynn prosecution, along with other politically sensitive national security cases — a level of second-guessing that has disturbed federal prosecutors in the Washington office and elsewhere.
Even some of Mr. Barr’s defenders acknowledge that the sentencing of Mr. Stone, a former campaign adviser to Mr. Trump, turned into a debacle for the department. Mr. Barr overruled the sentencing recommendation of four career prosecutors after Mr. Trump wrote on Twitter that Mr. Stone was being treated too harshly.
The prosecutors withdrew from the case in protest. Faced with a backlash in his department, Mr. Barr asked the president on national television to quit commenting on the department’s criminal cases, and associates suggested he was on the verge of resigning. But when Mr. Trump ignored him, Mr. Barr stayed put.
While Mr. Barr insisted he made his decision about Mr. Stone’s proper punishment based on the merits of the case, sentencing data show the move was extraordinary.
A jury convicted Mr. Stone, 67, of obstructing a congressional inquiry, tampering with a witness and lying to congressional investigators. The government requested that Mr. Stone be granted leniency despite the fact that he had refused to plead guilty.
That was the case in less than 2 percent of the nearly 75,000 criminal defendants who were sentenced in federal courts in the fiscal year that ended in September, according to data from the United States Sentencing Commission. The Stone case also stands out because the government ended up seeking a lighter punishment than the federal probation office had recommended, although that recommendation was likely guided by information provided by the prosecutors whom Mr. Barr overruled.
Prosecutor rarely ask for leniency after a trial because it undercuts their ability to negotiate guilty pleas with other defendants, according to Douglas A. Berman, a professor at Ohio State University’s Moritz College of Law who specializes in sentencing issues. “They want to be able to say, and to have a defense attorney repeat to a client, that they are willing to cut a deal, but they are never going to offer this again,” he said.
In fact, a review by The New York Times of more than 60 federal cases in which a defendant faced at least one similar charge to Mr. Stone’s turned up no instances in which the government recommended leniency after a trial. The Times reviewed cases in which defendants were sentenced after January 2017 and that were handled by two of the biggest U.S. attorneys offices: in Washington and in the central district of California.
In at least nine cases, the government asked for leniency, technically called a variance from sentencing guidelines. Prosecutors typically cited other mitigating factors, including advanced age or illness, on top of a speedy guilty plea.
Adam Goldman and Katie Benner contributed reporting. Susan Beachy contributed research.