Mr. Flynn’s lawyers recently told the president’s legal team that they could no longer discuss the special counsel’s investigation as they had been — a sign that Mr. Flynn had decided to cooperate with the prosecution. The investigation has dogged Mr. Trump’s first year in office.
Mr. Flynn is the fourth Trump associate to be charged. He was accused of making false statements to F.B.I. agents about two discussions with the Russian ambassador to the United States, Sergey I. Kislyak. Lying to the F.B.I. carries a penalty of up to five years in prison.
In one of the conversations described in court documents, the men discussed an upcoming United Nations Security Council vote on whether to condemn Israel’s building of settlements. At the time, the Obama administration was preparing to allow a Security Council vote on the matter.
Mr. Mueller’s investigators have learned through witnesses and documents that Israeli Prime Minister Benjamin Netanyahu asked the Trump transition team to lobby other countries to help Israel, according to two people briefed on the inquiry. Investigators have learned that Mr. Flynn and Mr. Trump’s son-in-law and senior adviser, Jared Kushner, took the lead in those efforts. Mr. Mueller’s team has emails that show Mr. Flynn saying he would work to kill the vote, the people briefed on the matter said.
In the other discussion, according to court documents, Mr. Flynn asked Mr. Kislyak that Moscow refrain from escalating the situation in response to sanctions announced by the Obama administration that day against Russia over its interference in the presidential election.
The F.B.I. interviewed Mr. Flynn at the White House four days after the president was sworn into office. American intelligence agencies had grown so concerned about Mr. Flynn’s communications with Mr. Kislyak and false accounts that he provided to Vice President Mike Pence that the acting attorney general at the time, Sally Q. Yates, warned the White House that its national security adviser might be compromised by the Russians.
Mr. Flynn served just 24 days, resigning on Feb. 13 after it was revealed that he had misled Mr. Pence and other top White House officials about his conversations with Mr. Kislyak.
But after accepting Mr. Flynn’s resignation, the president repeatedly said he thought Mr. Flynn was “a very good person” who had been treated poorly. The day after Mr. Flynn resigned, Mr. Trump told the F.B.I. director at the time, James B. Comey, “I hope you can see your way clear to letting this go, to letting Flynn go,” according to a memo Mr. Comey wrote describing that meeting.
In a news conference on Feb. 15, two days after Mr. Flynn’s resignation, the president blamed the media.
“General Flynn is a wonderful man. I think he has been treated very, very unfairly by the media, as I call it, the fake media in many cases,” Mr. Trump said. “And I think it is really a sad thing that he was treated so badly.”
But even before Mr. Trump said he would appoint Mr. Flynn as his national security adviser, questions swirled around Mr. Flynn’s connections to Russia, particularly a dinner he was paid to attend in Moscow in 2015 when he sat at the same table as Russian President Vladimir V. Putin.
Throughout the campaign, Mr. Flynn was an intense and vocal advocate of closer relations with Mr. Putin, arguing that the United States must work with the Russians to battle extremists. After he was named national security adviser, he continued to urge closer cooperation between the two nations.
The White House has said that Mr. Flynn has no information to provide prosecutors that would hurt Mr. Trump. A deal between Mr. Flynn and the special counsel is nonetheless significant. He was a key figure in the Trump campaign and the transition team. As Mr. Mueller tries to understand the behind-the-scenes story of those months, hearing from Mr. Flynn is important.
Mr. Flynn was a sometimes high-profile member of Mr. Trump’s campaign, often appearing on Fox News to advocate for the candidate’s foreign policy views.
Like Mr. Trump, Mr. Flynn was a brash, outspoken critic of former President Barack Obama, asserting that Shariah, or Islamic law, was spreading in the United States under his watch — a claim that was repeatedly debunked — and saying that the United States is in a “world war” with Islamist militants.
A controversial figure in the defense and intelligence community before joining Mr. Trump’s campaign, Mr. Flynn served as the head of Mr. Obama’s Defense Intelligence Agency. But he repeatedly clashed with Obama administration officials, who succeeded in persuading the former president to push him out of the intelligence job.
After he left the Obama administration, he formed a consulting group that led to inquiries into questionable lobbying for foreign governments, including the Turkish government, and hazy business ties with Middle Eastern countries.
Investigators working for the special counsel have questioned witnesses about Mr. Flynn’s dealings with the Turkish government and whether he was secretly paid by Turkish officials during the campaign. After he left the White House, Mr. Flynn disclosed that the Turkish government had paid him more than $500,000 to represent its interests in a dispute with the United States.
White House officials had been bracing for troublesome developments in the special counsel investigation, even as the president and some of his senior advisers had been saying in recent weeks that they believed Mr. Mueller was nearing the end of his probe.
Mr. Trump was not scheduled to make any public comments on Friday, though Mr. Flynn’s plea provided an awkward backdrop for remarks he was scheduled to give behind closed doors at an afternoon holiday reception with members of the news media.
An earlier version of this article said Michael T. Flynn, the former national security adviser to President Trump, had pleaded guilty to lying to the F.B.I. He was expected to plead guilty but had not entered a plea when the article was first published.
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