Press secretary Sean Spicer said the White House wanted to give Flynn, the former national security adviser, "due process" after Yates reported his call with a Russian ambassador about sanctions.
On the morning of January 26, acting Attorney General Sally Yates called White House counsel Don McGahn with a matter so sensitive it couldn't be discussed by phone.
After former Acting Attorney General Sally Yates and former Director of National Intelligence James Clapper testified on Capitol Hill Monday, President Trump took to Twitter to dismiss their revelations.
But here are four reasons why the entire Russian Federation story - as it relates to the 2016 election, to former Trump National Security Adviser Michael Flynn, and to any allegations of collusion - isn't fake news.
But McGahn had an odd response. His answer: "I'm not aware of any".
Trump said in a press conference three days after Flynn resigned, however, that when he looked at the information provided to him about Flynn's conversations with Kislyak, "I said, 'I don't think he did anything wrong".
During that time, Flynn was the most senior national security official in the West Wing, privy to every intelligence and foreign policy decision and secret, all the while, at risk of being blackmailed by Moscow, according to Yates.
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But Trump didn't move to fire Flynn. Yates had been fired during that gap.
The problem with that explanation is this: Yates talked to White House counsel Don McGahn about Flynn being compromised by the Russians on January 26 and January 27. But he didn't come that day, and that night Yates was sacked for refusing to implement Trump's order banning travelers from several majority-Muslim nations.
Flynn had multiple contacts with Kislyak during the transition, including an in-person meeting at New York's Trump Tower that was also attended by the president's son-in-law, Jared Kushner. We're going to have to depend on the Federal Bureau of Investigation, the press and Congress if we hope to get an answer. Monday's hearing further pumped the bellows.
Mr Pence said in January that Mr Flynn denied those calls involved sanctions placed on Russian Federation by the Obama administration in response to its election meddling. Clapper said he was not "aware of any instance" of unmasking being used for political purposes.
During that section of the hearing, Clapper described as accurate a report in the Guardian newspaper that British intelligence officials became aware in late 2015 about suspicious interactions between Trump advisers and Russian agents, and that the information was passed on to US intelligence agencies.
What happened in the 18 days between when the White House received a warning about Flynn and his firing?And could he see the evidence?
"We were giving them [White House officials] this information so they could take action".