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Mr. Trump has been preoccupied with the investigation into Mr. Flynn since at least early last year. In February 2017, alone in the Oval Office with the F.B.I. director at the time, James B. Comey, the president asked him to end the investigation, Mr. Comey told lawmakers. After that episode became public, Mr. Mueller was appointed by the Justice Department to be the special counsel.

On the day after Mr. Flynn pleaded guilty, the president wrote in a Twitter post said to be composed by Mr. Dowd that he fired Mr. Flynn for, among other things, lying to the F.B.I. But Mr. Trump continued to publicly defend his former national security adviser, saying two days later that he felt “very badly” for Mr. Flynn and that the F.B.I. had “destroyed his life.”

It is not clear what Mr. Flynn has told the special counsel as part of his cooperation agreement. During interviews with other witnesses, Mr. Mueller’s investigators have focused on what Mr. Flynn told the president about his calls during the transition with the Russian ambassador to the United States at the time, Sergey I. Kislyak. The calls came soon after the Obama administration announced new sanctions on Russia for its role in disrupting the 2016 presidential campaign.

Mr. Manafort, who ran Mr. Trump’s presidential campaign for several months, has been indicted on dozens of counts of money laundering and other financial crimes connected to his work as a lobbyist and former consultant for Viktor F. Yanukovych, who at the time was president of Ukraine. The charges are not connected to any work that Mr. Manafort did for Mr. Trump.

Rick Gates, who was Mr. Manafort’s business partner for years and also served as deputy chairman of the Trump presidential campaign, pleaded guilty last month as part of a cooperation agreement with Mr. Mueller’s team. On the day the plea agreement was announced, Mr. Manafort vowed to continue to fight the charges against him.

In total, 19 people have been charged with crimes by Mr. Mueller. Five of them, including Mr. Flynn and two other Trump associates, have pleaded guilty and have agreed to cooperate.

In August, Mr. Trump pardoned Joe Arpaio, the former sheriff from Arizona who had been found guilty of federal criminal contempt for refusing to stop targeting Latinos in traffic stops and other law enforcement efforts. The pardon prompted an outcry because Mr. Arpaio, whose crackdown on illegal immigration made him a national symbol for both conservatives and liberals, had supported Mr. Trump’s run for president.