In September, a federal judge on set Flynn's sentencing for December 18, more than a year after the retired U.S. Army lieutenant general pleaded guilty to lying to the FBI about his contacts with Russian Federation during the presidential transition. The former New York City mayor lambasted the Mueller team as "overzealous media-inspired prosecutors".
Prosecutors said in a court filing that Flynn had provided "substantial assistance" in Mueller's probe, including giving "firsthand information about the content and context of interactions between the transition team and Russian government officials".
Frustratingly, the document outlining just how Flynn has helped is heavily redacted because it "includes sensitive information about ongoing investigations".
The sentencing memo was "respectfully submitted" by special counsel Mueller himself.
His cooperation in one criminal investigation has been fully redacted. One knowledgeable source said the bulk of Flynn's cooperation with the special counsel occurred immediately following his December court appearance.
Flynn's false statements stemmed from a January 24, 2017, interview with the Federal Bureau of Investigation about his interactions with Sergey Kislyak, Russia's then-ambassador to the US, as the Obama administration was levying sanctions on the Kremlin in response to election interference.
He is due to be sentenced in the US District Court for the District of Columbia on 18 December. Two others who admitted to lying to investigators in Mueller's probe ended up with light sentences even though they didn't cooperate with prosecutors.
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Prosecutors said the two men discussed USA sanctions against Russian Federation and that Flynn also asked Kislyak to help delay a United Nations vote seen as damaging to Israel.
During those conversations with Mr Kislyak, Mr Flynn asked Moscow to delay or vote against the resolution, a request the Kremlin ultimately rejected. That conversation took place the day the Obama Administration announced it was imposing sanctions on Russian Federation for attempting to interfere in the election, raising questions about whether he violated the Logan Act, which bars private citizens from negotiating with foreign governments about official disputes.
Flynn's cooperation could be trouble for people around Trump. Both of those matters had been previously referenced in the court filings and hearings for Flynn's plea a year ago.
The former National Security Adviser, who resigned on February 13 2016, only weeks after Trump's inauguration, also lied about registering as someone working for the Turkey government under the Foreign Agents Registration Act (FARA).
So far Trump has defended Flynn publicly, including in an April tweet.
Mueller's team credited Flynn with serving 33 years in the U.S. Army, including five years in combat.
Once he entered the private sector, Flynn launched his own security consulting firm, Flynn Intelligence Group, and used his military experience to enter a wide range of business ventures, some which involved problematic entanglements.
"He realises that he needs to move on with his life, and that he'd like to begin that process as soon as possible", said Andrew W. Albstein, a lawyer and friend who wrote a letter of support on Cohen's behalf to the judge.
Another branch of Mueller's investigation is also emerging - his interest in alleged communications between Trump's informal political adviser Roger Stone and associate Jerome Corsi with WikiLeaks, the website that published emails stolen by Russian spies from the Clinton campaign's chairman and the Democratic National Committee.