Michael Flynn Wasn't Fired by Donald Trump Even After Learning He Was Under Investigation: Report

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National security adviser General Michael Flynn arrives to deliver a statement during the daily briefing at the White House in Washington, D.C., on February 1. A new report claims President Donald Trump did not fire Flynn even after learning that he was under investigation by the Justice Department. Carlos Barria/Reuters

Weeks before his inauguration, Donald Trump's transition team learned that the Justice Department was investigating the president-elect's national security adviser, Michael Flynn, for surreptitiously working as a lobbyist for Turkey, The New York Times reported on Wednesday.

Citing two sources familiar with the case, the report indicates the Trump team knew about Flynn's legal problems on January 4, earlier than previously reported, and still gave him access to top-level intelligence. Flynn had learned of the probe roughly a month earlier and told the Trump team's main lawyer, Donald McGahn. 

Related: Why Mike Flynn is a security risk

About 10 days before inauguration, McClatchy reports that Flynn made one of his first decisions as national security adviser: delaying the Defense Department's plan to retake Raqqa, the main stronghold of the Islamic State group (ISIS), along with Kurdish forces in Syria. The Pentagon considered those forces critical, and the Obama administration asked for the Trump team's sign-off. Flynn, however, asked for a delay, which pushed the operation back by months. It's unclear why the retired general did so. But as McClatchy explains, the Turkish government opposes the U.S. arming the Syrian Kurds—something the Trump administration later decided to do anyway. 

The White House has not commented on either story. 

The revelations come at a trying time for the embattled Trump administration. On Tuesday, The New York Times reported the president asked FBI Director James Comey to drop the investigation into Flynn, who took money from both the Russian and Turkish governments without disclosing it.

The president had fired Comey the week prior, leading some to question whether he was trying to squash not only the Flynn probe, but also a separate investigation into the Trump campaign's alleged collusion with Moscow during the 2016 election. 

On Monday, The Washington Post reported that Trump had leaked top-secret information about ISIS to two Russian officials, even though the U.S. had obtained it through a sensitive intelligence-sharing agreement with an American ally. Other outlets later reported that ally was Israel. 

Democrats, and even a few Republicans, responded with outrage to the barrage of news. In a biting speech on the House floor Wednesday, Representative Al Green, a Democrat from Texas, called for Trump's impeachment. The president has remained defiant, calling the investigations and reports bogus and unfair.

Yet late on Wednesday, before the two stories about Flynn broke, the Justice Department announced it would appoint Robert Mueller III, the former head of the FBI, as a special counsel to lead the Trump probes, which include other campaign officials besides Flynn.

Acting FBI Director Andrew McCabe, Comey's replacement, has called the collusion investigation "highly significant." In the New York Times story about Flynn on Wednesday, the paper reported details about a grand jury inquiry in Virginia that's looking into the retired general's foreign ties. Among them: Brandon Van Grack, a longtime espionage prosecutor, is leading the inquiry and has issued subpoenas to companies that worked with Flynn and others. 

Citing people who have talked to the retired general, the paper also reported that Flynn—whom Obama fired as the head of the Defense Intelligence Agency in 2014—believes the previous administration started to investigate his activities to keep him out of the White House. 

Not long after Trump won the 2016 election, Obama reportedly warned the president-elect about bringing on his ex-DIA chief, but Trump, who became close with Flynn during the campaign, decided to hire him as his national security adviser.

Months later, in February, Flynn stepped down. His resignation followed a report in The Washington Post that said he had discussed ending sanctions against Moscow in a meeting with the Russian ambassador before the inauguration. That account ran counter to what Flynn had apparently told Trump administration officials about the meeting, and the president subsequently asked him to resign. 

Acting Attorney General Sally Yates later testified she had warned the White House about Flynn's false statements regarding his discussions with the ambassador, Sergey Kislyak, and how they left him vulnerable to blackmail by Moscow. The White House disputes this account. 

Flynn is now being investigated for the Kislyak affair as well.