There’s a section of Flynn’s plea deal that says:
“d) Your client acknowledges and understands that, during the course of the cooperation outlined in this Agreement, your client will be interviewed by law enforcement agents and/or Government attorneys. Your client waives any right to have counsel present during these interviews and agrees to meet with law enforcement agents and Government attorneys outside of the presence of counsel.”
Who agrees to meet with Mueller without counsel present?
Mueller obviously had the goods on Flynn, and could have charged him with something (I have no idea what) much more serious than this chicken$hit "lying to the FBI about something that wasn't a crime" charge. So Flynn agreed to plead and to become a snitch for Mueller against someone higher up. I don't know who but, if I had to guess, I'd say probably against Kushner.
This is the way white-collar criminal investigations work-- you find someone you can charge with something, get them to testify against someone higher up, then go to that person and tell them what they could be charged with, and keep repeating the process.