Mueller's investigation is supposed to be about Russian hacking in the November 2016 election, but Flynn is pleading guilty to lying about speaking to the Russian ambassador in December,
after the election. Talking to other govt's would normally be completely legal and normal for an incoming administration, so on the surface, Flynn was just doing his job.
No one yet knows why Flynn lied to both the FBI
and Pence about a totally legitimate and legal discussion with Kislyak, but perhaps it is related to his failure to register as a foreign agent for Turkey. When Trump found out Flynn lied, he fired Flynn, which he tweeted recently. There is some speculation Flynn got frightened by a Logan Act accusation since he wasn't yet officially a part of the govt. Maybe.
The FBI had a FISA tap on Flynn, Manafort, etc., (which Trump complained about at the time, that his phones were tapped, was poo-pooed) and they knew Flynn'd been with
Kisoff, I mean Kislyak, but they got Flynn into a compromising position and made a Martha Stewart out of him.
How did Trump know Flynn lied around the same time as the FBI? Maybe someone inside the FBI thought that using a bogus FISA warrant to snoop on the Trump campaign was a perversion of democracy? Maybe someone inside the Clinton campaign who had previously leaked? Someone no longer with us?
Investigation so far has revealed Facebook, Twitter and a disorganized Ukranian bot farm did legal things to "influence" the election, while one of the FBI's lead investigators was removed and demoted for anti-Trump bias and the FBI refused Congress' request about this for months. Keep investigating.