WASHINGTON — After announcing that the Justice Department was dropping the criminal case against Michael T. Flynn, the former national security adviser, Attorney General William P. Barr was presented with a crucial question: Was Mr. Flynn guilty of lying to the F.B.I. about the nature of phone calls he had with the Russian ambassador to the United States?

After all, Mr. Flynn had twice pleaded guilty to lying about them.

“Well, you know, people sometimes plead to things that turn out not to be crimes,” Mr. Barr said in an interview with CBS News. Then he went even further and described the infamous calls during the Trump presidential transition as “laudable.”

Mr. Trump and his allies now accuse the F.B.I. of framing Mr. Flynn, which is part of the president’s broader campaign to tarnish the Russia investigation and settle scores against perceived enemies ahead of the November election.

Their revisionist narrative is in stark contrast to the view held three years ago not only by top F.B.I. management but also by senior White House officials. Mr. Flynn, the officials said then, had lied to Vice President Mike Pence and other aides about the nature of his calls to the ambassador, had lied repeatedly to F.B.I. agents about the calls, and might have made himself vulnerable to Russian blackmail.

Revisiting the chaotic weeks surrounding Mr. Flynn’s ouster — based on recently disclosed government documents, public statements, court records and interviews — show how much the original Trump administration concerns about him have been buried under the president’s cause of portraying the Russia investigation as a “witch hunt.”

Mr. Barr, for example, has recently argued that the F.B.I. interview of Mr. Flynn was not justified because agents who had been investigating him had not found any wrongdoing and were on the verge of closing the case. When agents found out about the call with the Russian ambassador, Sergey I. Kislyak, they concocted a reason to keep the case open for “the express purpose of trying to catch, lay a perjury trap for General Flynn,” Mr. Barr said in the CBS interview.

A broad array of legal experts disagree. “This case reeks of political influence,” said Marshall L. Miller, a former top prosecutor in Brooklyn and the principal deputy of the Justice Department’s criminal division. “Mr. Flynn admitted twice under oath that he lied to the F.B.I. Political appointees at D.O.J. are now trying to rewrite the law to erase the crime.”

Mr. Flynn’s troubles began with a phone call.

It was Dec. 29, 2016, the day the outgoing Obama administration announced sanctions against Russia for the country’s widespread effort to disrupt the 2016 presidential election. Mr. Flynn, who was Mr. Trump’s incoming national security adviser, urged Mr. Kislyak in a phone call not to escalate tensions with a retaliatory move against the United States — perhaps by kicking American diplomats and spies out of Russia.

Given the circumstances, the call was remarkable. The United States government had just determined that its longtime adversary had launched a concerted effort to sabotage a presidential election, and the incoming national security adviser was having a back-channel discussion with a top Russian official that might lead to the new Trump administration gutting the sanctions its predecessor put in place to punish the Russians.

Mr. Flynn chose not to document the calls with the ambassador, a decision that records from the investigation of the special counsel, Robert S. Mueller III, show was based on his concern that he might be interfering with the Obama administration’s foreign policy weeks before Mr. Trump took office. His concerns were well founded. When President Vladimir V. Putin of Russia did not retaliate after the Obama administration’s sanctions, President Barack Obama was perplexed and asked spy agencies to figure out why.

The F.B.I. unearthed the discussions between Mr. Flynn and Mr. Kislyak when reviewing transcripts of the ambassador’s intercepted calls. F.B.I. officials discussed interviewing Mr. Flynn, whom agents had been investigating as part of the bureau’s inquiry into whether any Trump campaign associates had conspired with Russia during the presidential election.

Top Trump transition officials — including Mr. Pence as well as Reince Priebus, who was to be White House chief of staff, and Sean Spicer, the incoming White House press secretary — questioned Mr. Flynn about the Washington Post column. Mr. Flynn denied that he spoke about sanctions with Mr. Kislyak, and Mr. Spicer repeated those claims to members of the news media.

Days later, on Jan. 15, 2017, Mr. Pence was asked about the column during an interview on the CBS News program “Face the Nation.” The incoming vice president said that he had talked with Mr. Flynn about his calls with Mr. Kislyak, and he said that Mr. Flynn was unequivocal. “They did not discuss anything having to do with the United States’ decision to expel diplomats or impose censure against Russia,” the vice president said.

Mr. Pence’s interview set off alarms at the F.B.I. and the Justice Department. If Mr. Flynn had lied to the vice president, the Russians knew that and could use it as leverage over Mr. Flynn. Newly disclosed documents made public in Mr. Flynn’s criminal case show officials were also concerned that Mr. Pence might have been lying, as well.

“The implications of that were that the Russians believed one of two things — either that the vice president was in on it with Flynn, or that Flynn was clearly willing to lie to the vice president,” Mary B. McCord, a former top national security at the time, said in an interview with the special counsel’s office.

The F.B.I. decided to try to find out who was lying to whom. James B. Comey, the bureau’s director at the time, sent a pair of agents to the White House to speak with Mr. Flynn, who by then was only a few days into his job as national security adviser. But Mr. Comey made the unusual decision to not notify senior Justice Department officials about the interview until the agents were already on their way to the White House — blindsiding and infuriating the officials who oversee the F.B.I. about a highly sensitive session.

During the interview, Mr. Flynn was asked about sanctions and other topics. He denied talking about Russian sanctions, according to documents, even as agents used his own words from the highly classified transcripts to refresh his memory. Mr. Flynn seemed relaxed, agents would note, and did not betray any signs of deception.

But the F.B.I. reports from the interview did not square with the transcripts of the phone calls, and soon Trump administration lawyers were discussing whether Mr. Flynn might have committed a felony by making false statements during the interrogation.

Mr. Priebus later recounted to Mr. Mueller’s investigators a meeting with Mr. Trump in which he told the president about the concerns that Mr. Flynn had lied during his F.B.I. interview. Mr. Trump was angry, Mr. Priebus recalled, and said, “Not again, this guy, this stuff.”

Within days, White House lawyers — including the White House counsel, Donald F. McGahn II — had concluded, after reviewing the transcripts of the calls, that Mr. Flynn had repeatedly lied about his discussions with Mr. Kislyak. According to the findings by the special counsel, “McGahn and Priebus concluded that Flynn could not have forgotten the details of the discussions of sanctions and had instead been lying about what he discussed with Kislyak.”

Mr. McGahn and Mr. Priebus decided that Mr. Flynn needed to go and made that recommendation to Mr. Trump.

On Feb. 13, after Mr. Priebus told Mr. Flynn that he must resign, he brought him into the Oval Office. There, Mr. Flynn and the president hugged, and Mr. Trump said he would give Mr. Flynn a good recommendation. “You’re a good guy,” the president said, according to the account Mr. Priebus gave to the Mueller team. “We’ll take care of you.”

Ten months later, after Mr. Flynn had pleaded guilty for lying to the F.B.I. agents and agreed to cooperate with the Mueller investigation, Mr. Pence said that removing him from the White House was the right move.

“What I can tell you is that I knew that he lied to me,” the vice president told CBS News, “and I know the president made the right decision with regard to him.”

Mr. Pence no longer holds that view, and his change over time reflects the far more combative position among Trump administration officials toward the various investigations into Mr. Trump and his advisers.

As this shift was occurring, Mr. Flynn jettisoned the legal team that had advised him to cut a deal with the Mueller prosecutors and hired a new lawyer, Sidney Powell, who launched a frontal attack on the forces that she believed led her client into wrongfully admitting to a felony offense.

In a letter to Mr. Barr last June, days before officially becoming Mr. Flynn’s lawyer, Ms. Powell wrote that “it is increasingly apparent that General Flynn was targeted and taken out of the Trump administration for concocted and political purposes.” The letter was disclosed last year by federal prosecutors in the Flynn case.

After Mr. Barr announced his decision last week to drop criminal charges in the Flynn case, top Trump administration officials — including those who three years ago believed most vehemently that he should be fired — said that he would be welcomed back at the White House.

“I think General Michael Flynn is an American patriot; he served this country with great distinction,” Mr. Pence said last week in an interview with Axios. “And for my part, I’d be happy to see Michael Flynn again.”

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