After an extraordinary public campaign by President Trump and his allies, the Justice Department dropped its criminal case on Thursday against Michael T. Flynn, Mr. Trump’s first national security adviser.

Mr. Flynn had previously pleaded guilty twice to lying to F.B.I. agents about his conversations with a Russian diplomat during the presidential transition in late 2016.

The move was the latest example of Attorney General William P. Barr’s efforts to chisel away at the results of the Russia investigation. Documents that Mr. Flynn’s lawyers cited as evidence of prosecutorial misconduct were turned over as part of a review by an outside prosecutor whom Mr. Barr assigned to re-examine the case. Mr. Barr has cast doubt not only on some of the prosecutions in the investigation but also on its premise, assigning another independent prosecutor to scrutinize its origins.

The decision for the government to throw out a case after a defendant had already pleaded guilty was also highly unusual. Former prosecutors struggled to point to any precedent and portrayed the Justice Department’s justification as dubious.

By abandoning the case, the department undid what had been one of the first significant acts of the special counsel investigation into possible ties between the Trump campaign and Russia’s 2016 election interference — the prosecution of a retired top Army general turned national security adviser who pleaded guilty to lying to investigators.

Though Mr. Trump fired Mr. Flynn weeks into his presidency for lying to Vice President Mike Pence about the conversations with the diplomat, he has long complained that a corrupt few at the F.B.I. mistreated Mr. Flynn and suggested he might pardon him. Law enforcement officials dropping the charges took issue with the F.B.I.’s interview of Mr. Flynn in early 2017 as part of the Russia investigation that Robert S. Mueller III later took over.

Agents’ questioning “was untethered to, and unjustified by, the F.B.I.’s counterintelligence investigation into Mr. Flynn,” the acting United States attorney in Washington, Timothy Shea, wrote in a motion to dismiss the charges. Prosecutors said that the case fell short of the legal standard that Mr. Flynn’s lies be “materially” relevant to the matter under investigation.

“The government is not persuaded that the Jan. 24, 2017, interview was conducted with a legitimate investigative basis and therefore does not believe Mr. Flynn’s statements were material even if untrue,” Mr. Shea wrote.

Democrats condemned the move. “A politicized and thoroughly corrupt Department of Justice is going to let the president’s crony simply walk away,” said Representative Jerrold Nadler, Democrat of New York and the chairman of the House Judiciary Committee. “Americans are right to be furious and worried about the continued erosion of our rule of law.”

He said he would ask the Justice Department inspector general to investigate and work to secure Mr. Barr’s testimony before his committee as soon as possible.

In dropping the charges, law enforcement officials abandoned the stance of the career prosecutors who had been on the case, who had argued that Mr. Flynn’s conversations with the Russian ambassador to the United States at the time, Sergey I. Kislyak, “went to the heart” of the F.B.I.’s Trump-Russia investigation.

Mr. Trump told reporters on Thursday that Mr. Flynn was “an innocent man” and accused Obama administration officials of targeting him to try to “take down a president.” He angrily tore into his unnamed persecutors. “I hope a lot of people are going to pay a big price because they’re dishonest, crooked people,” Mr. Trump said. “They’re scum — and I say it a lot, they’re scum, they’re human scum. This should never have happened in this country.”

Mr. Barr explained the decision as an effort to “restore confidence in the system” and that law enforcement officials had a duty to dismiss the charges. He said he was “doing the law’s bidding,” not Mr. Trump’s, and the Justice Department said that it did not brief the White House before it dropped the charges.

“Partisan feelings are so strong that people have lost any sense of justice,” Mr. Barr said in an interview with CBS News.

Asked whether Mr. Flynn lied, Mr. Barr said that “people sometimes plead to things that turn out not to be crimes.”

Sidney Powell, Mr. Flynn’s lawyer, said on Fox Business Network that she and her client were “relieved and gratified” that Mr. Barr withdrew the case. She called the decision “a restoration of the rule of law.”

Mr. Flynn pleaded guilty in December 2017 to lying to the F.B.I. about his conversations with Mr. Kislyak during the presidential transition. He had also entered a guilty plea a second time in 2018 at an aborted sentencing hearing. At the time, Mr. Flynn said he knew that lying to the F.B.I. was a crime and accepted responsibility for what he had done.

The climactic move by the Justice Department appeared to be brewing in recent days after the outside prosecutors reviewing the case said they had found new documents that were possibly exculpatory, raising the hopes of Mr. Flynn’s lawyers and vocal supporters that he would be exonerated.

One of the documents showed that the F.B.I. was on the verge of closing a counterintelligence investigation into Mr. Flynn’s ties to Russia in early January 2017. Mr. Shea, a longtime trusted adviser of Mr. Barr’s, said in the court filing that F.B.I. agents had no reason to interview Mr. Flynn at the White House weeks later.

In a possible sign of disagreement, Brandon L. Van Grack, the Justice Department lawyer who led the prosecution of Mr. Flynn, abruptly withdrew from the case on Thursday. Mr. Flynn’s lawyers have repeatedly attacked Mr. Van Grack by name in court filings, citing his “incredible malfeasance.” Other prosecutors in Mr. Shea’s office were stunned by the decision to drop the case, according to a person who spoke with several lawyers in the office.

Neither Mr. Van Grack nor other career prosecutors who have worked on the Flynn case over the past two and a half years signed their names to Mr. Shea’s court filing.

It is now up to the federal judge in Washington overseeing the case, Emmet G. Sullivan, to decide whether to dismiss it and close off the possibility that Mr. Flynn could be tried again for the same crime. If the judge wants, he could ask for written submissions and hold a hearing on that topic.

Judge Sullivan, who accepted Mr. Flynn’s original guilty plea, could also weigh in on whether he believes any of the new materials that the government has produced to Mr. Flynn’s lawyers represent a violation on the part of the Justice Department or its lawyers who worked on the case.

The White House was prepared for the possibility of Mr. Trump pardoning Mr. Flynn last week, according to two people familiar with the discussions. But some advisers urged the president to let the case play out.

Mr. Flynn, a decorated lieutenant general and former head of the Defense Intelligence Agency, was an early supporter of Mr. Trump’s 2016 presidential campaign, joining the crowd in a “lock her up” chant about Hillary Clinton, then the presumptive Democratic presidential nominee, at the Republican National Convention that year.

After winning the election, Mr. Trump named Mr. Flynn his national security adviser. In late December 2016, Mr. Flynn and Mr. Kislyak spoke on the phone shortly after the Obama administration placed sanctions on Russia for interfering in the election, and Mr. Flynn advised that the Russians hold off on escalating in response, undermining that administration’s foreign policy.

The F.B.I. had been close to closing its inquiry into Mr. Flynn. But as investigators discovered the conversations in early January through routine government wiretaps of Mr. Kislyak, and as they learned in subsequent days that he had lied to other White House officials about them, they began to conclude that they had reason to suspect that Mr. Flynn constituted a national security threat.

Law enforcement officials warned the White House that Russia could have blackmailed Mr. Flynn. But seeing no move by Mr. Trump to address the issue, F.B.I. agents decided to question Mr. Flynn, where he repeatedly made false statements about his talks with Mr. Kislyak.

Yet the agents “felt like it was not clear to them that he was, you know, lying or dissembling,” Andrew G. McCabe, the F.B.I. deputy director at the time, told congressional investigators in an interview released on Thursday as part of thousands of pages of witness testimony from the House Intelligence Committee’s own Russia inquiry.