The answer appears to be pretty simple. The NY Times reported that “he had misled Vice President Mike Pence and other top White House officials about his conversations with the Russian ambassador to the United States.”
Mr Flynn had claimed that his conversation with ambassador Mr Kislyak in December was limited to “small talk and holiday pleasantries” but according to officials privy to the transcript of the wire tap the conversation included talk of sanctions imposed on Russia in 2016 over allegations of interference in the U.S. elections on Mr Trump’s behalf.
The officials also said however that the transcript was ambiguous enough they believed Mr Trump “could have justified either firing or retaining Mr Flynn.”
Apparently Mr Trump’s concern over the media storm surrounding Mr Flynn and the negative impact it may have on people’s perception of his stance on national security issues led to the president’s chief strategist asking for his Mr Flynn’s resignation on Monday.
The White House had previously defended Mr Flynn’s claims but a former administration official said that “the Justice Department warned the White House last month that Mr. Flynn had not been fully forthright about his conversations with the ambassador. As a result, the Justice Department feared that Mr. Flynn could be vulnerable to blackmail by Moscow.”
The article also referenced Flynn’s resignation letter in which he stated;
“Unfortunately, because of the fast pace of events, I inadvertently briefed the vice president-elect and others with incomplete information regarding my phone calls with the Russian ambassador,” “I have sincerely apologized to the president and the vice president, and they have accepted my apology.” “I am tendering my resignation, honoured to have served our nation and the American people in such a distinguished way,”
He is to be replaced by Lt. Gen. Joseph K. Kellogg Jr. a retired Vietnam War veteran although it is unlikely Mr Kellogg will remain in the position. According to an anonymous source close to the administration “retired Vice Admiral Robert S. Harward is the leading candidate to replace Mr. Flynn, although Mr. Kellogg and David H. Petraeus are being discussed.”
Mr FLynn’s resignation has sparked much conversation and debate over Mr Trump’s involvement with Russia and had led to calls for investigations into the presidential administration’s intentions towards Vladimir Putin’s Russia even after the invasion of Ukraine last year.
The timing couldn’t be worse as Mr Trump has yet to offer a plan on how to combat IS and other radical Islamists he’s claimed are the number 1 threat to the U.S. and he and Mr Pence along with other senior officials prepare for meetings with foreign leaders, starting this week in Europe.
One thing's for sure, it has added fuel to his critics fire with #TrumpImpeachmentParty trending world wide this morning.
Sources:
https://www.nytimes.com/2017/02/13/us/politics/donald-trump-national-security-adviser-michael-flynn.html?_r=0
https://www.bloomberg.com/politics/articles/2017-02-14/flynn-departure-leaves-trump-national-security-team-in-turmoil