Apparently the Russian that Flynn contacted was Sergey Kislyak, the a Russian Ambassador in DC at the time. Not sure it can stretch to a treason charge to talk to a diplomat, although lying to the FBI is definitely illegal. Anyways, the conversation Flynn and Kislyak had was about whether or not to condemn the latest Israeli settlements in Palestine. Trump wanted Russia on board to kill the vote (and hook up Kushner).

As far as "the real story" goes, however, the bit about Flynn getting paid 530k by an Erdogan associate to investigate Fetullah Gulen is likely what concerns Mueller more, as anyone investigating Gulen has a risk of stumbling on to the same things Sibel Edmonds did. If you'll recall, Mueller was the FBI chief at the time Edmonds blew the whistle on the FBI for covering up money laundering through Gulen-linked charities which wound up funding 9/11 hijacker prep.