Flynn was a longtime adversary of the Obama admin. He was a sole dissenter among Obama's sycophants, and as DIA chief, he was privy to much of the fuckery perpetrated. He had a target on his back for many years.

When he joined the campaign and Trump ultimately won the election, the Obama admin had to keep Flynn the fuck away from any federal office which would allow him to expose the treachery they had committed leading up to, during and after the election of 2016.

During the transition, a Russian interference pretense was engineered, Obama kicks the Russian diplomats from the country, prompting a call from the Ruskie ambassador Kislyak to his counterpart in the incoming administration (Flynn). I would argue this was done with the intent of prompting the call, which could then be spied on (this did happen) and the transcript could be used to entrap Flynn if they can't nail him for anything explicitly said in the call. They were hoping to find anything they would be able to paint as "collusion", failing that a trap could be set. FBI looks at the call, finds nothing illegal, tries to close the case, "7th floor" (Comey/McCabe) intervene to keep the case open, and an interview is done at the White House.

The interviewers, Strzok and Priestap Pientka, have a transcript of the call (unknown to Flynn at the time) which they then start grilling him on. Original 302 of the interview (since "lost", but edit history remains) recorded that Flynn showed "no signs of deception". Weeks go by, 302 gets edited and bastardized, and all the sudden they decide to try to charge him, coerce him to plead by threatening to go after his son.

Rest is history.