The special counsel Robert Mueller sent a big message this week: cooperate with investigators and they'll show you leniency. Refuse, and they'll bite back.

Mueller's office recommended little to no jail time for former national security adviser Michael Flynn, who they said provided "substantial assistance" to multiple ongoing investigations, including the Russia probe.

Flynn's sentencing memo was heavily redacted, but one DOJ veteran said that "if you read around all that black ink, Mueller did say enough to let us know this: Flynn gave up the goods, and Mueller's work is far from over."

President Donald Trump's former lawyer, Michael Cohen, also pleaded guilty in the Russia probe last week and has shown a keen willingness to tell prosecutors everything he knows.

Cohen's and Flynn's cases stand in stark contrast to that of former Trump campaign chairman Paul Manafort, who prosecutors accused of breaching his plea deal and committing additional crimes after pleading guilty.

The special counsel Robert Mueller sent a clear message this week: cooperate with investigators and be forthcoming about what you know, and they'll show you leniency. Refuse, and they'll bite back.

Late Tuesday, prosecutors filed a highly anticipated sentencing memorandum in the case of former national security adviser Michael Flynn, who pleaded guilty last year to lying to the FBI.

In it, they recommended that Flynn get little to no jail time, citing the "substantial assistance" he provided to the special counsel's investigation into Russia's interference in the 2016 election, as well as other, separate ongoing investigations.

Flynn was among the first defendants to plead guilty in the Russia probe and has been cooperating with Mueller for over a year. His sentencing was delayed five times after prosecutors said they needed more information from the former national security adviser, who also served as a key adviser to President Donald Trump's 2016 campaign.

In their Tuesday filing, prosecutors emphasized that Flynn began cooperating early, that his assistance was critical in encouraging other witnesses to come forward and be candid, and that he helped the investigation in several ways.

Michael Flynn. Jonathan Ernst/Reuters

'Flynn gave up the goods'

In typical fashion, Mueller's office revealed very little information, if any, about the specifics of what Flynn told them. Prosecutors also attached a largely-redacted 6-page addendum to the sentencing memo laying out how Flynn had cooperated in what appears to be a separate investigation not being conducted by Mueller's office.

In the original sentencing memo, prosecutors laid out the crux of what Flynn was charged with: his lies to the FBI about conversations he had during the transition period with then-Russian ambassador Sergey Kislyak about US sanctions on Russia.

But that's not the only thread of which Flynn may have had valuable information.

The former national security adviser was also not forthcoming about his involvement in three key areas: his now defunct lobbying firm's work for the Turkish government in 2016, his efforts with Russia and Saudi Arabia to develop nuclear reactors in the Middle East, a project that would have benefited from the US lifting sanctions on Russia, and payments he received from the state-owned media outlet Russia Today that he failed to disclose when he applied to renew his security clearance in January 2016.

Flynn was also a participant in a controversial meeting with Kislyak and senior adviser Jared Kushner during the transition period, in which Kushner reportedly discussed setting up a secret back channel between the Trump team and Moscow using Russian diplomatic facilities.

And he served as an adviser to the campaign when Kushner, then campaign chairman Paul Manafort, and Donald Trump Jr. met with two Russian lobbyists offering dirt on the Hillary Clinton campaign. The meeting, which took place at Trump Tower in June 2016, is a key investigative focus for the special counsel and congressional committees.

Flynn's sentencing memo said he provided "firsthand information" about contacts between Russian officials and members of the Trump transition team.

"We do not yet know everything about Flynn's cooperation," said Elie Honig, a former federal prosecutor from the Southern District of New York, in an interview with INSIDER. "The heavy redactions in the filing hide nearly all the details that Mueller provided to the court."

Jens David Ohlin, a vice dean at Cornell Law School and an expert on criminal law, echoed that view.

"There is more to come, but we don't know what that is," told INSIDER. The substantial redactions in Flynn's sentencing memo indicate that the targets of other investigations he's cooperated with have not yet been charged, he said. "It could be a reference to an obstruction of justice investigation, possibly involving the president, but we don't really know. So this is a known unknown."

Honig emphasized, however, that "if you read around all that black ink, Mueller did say enough to let us know this: Flynn gave up the goods, and Mueller's work is far from over."

Paul Manafort with Trump senior adviser Stephen Miller Drew Angerer/Getty Images

'Manafort tried to play both sides and got caught'

To be sure, Mueller recently secured a guilty plea from another crucial player: Trump's former longtime lawyer and fixer, Michael Cohen, who pleaded guilty last week to one count of lying to Congress in 2017.

Like Flynn, Cohen has signaled a willingness to tell prosecutors everything he knows in exchange for leniency. His first meeting with Mueller came in early August, before he pleaded guilty to separate charges in a Manhattan US attorney's office investigation into his and Trump's financial dealings before the 2016 election.

Cohen has voluntarily met with Mueller's team, New York prosecutors, and investigators in the New York attorney general's office several times since, his lawyers said.

They also dropped a number of bombshells about what Cohen knows in a sentencing memo they filed on his behalf last week. Cohen has asked for an early sentencing date so he can go about rebuilding his life, his lawyers said, but that does not signal that he doesn't want to help the investigation.

On the contrary, they said, "he expects to cooperate further."

Jeffrey Cramer, a longtime former federal prosecutor who spent 12 years at the Justice Department, told INSIDER the fact that Cohen and Flynn both pleaded guilty to lying to investigators and have cooperated extensively is a key indication that Mueller is gaining traction.

"When you see people pleading guilty or getting indicted on similar facts, that's when you start building a path forward as a prosecutor," he said.

Michael Cohen. Drew Angerer/Getty Images

The Cohen and Flynn memos stand in stark contrast to what prosecutors said about Manafort, whom they accused last month of breaching his plea deal by lying to investigators after pleading guilty and allegedly committing more crimes. They were also reportedly furious when they learned that Manafort's lawyers were regularly in touch with Trump's lawyers about what Manafort was being questioned about.

Prosecutors are expected to lay out Manafort's alleged misdeeds in intricate detail in a court brief Friday. And Politico reported that the special counsel is weighing putting Manafort on trial again in the wake of his decision to breach his plea deal.

"Even if Manafort decides to cooperate now, there's no chance Mueller accepts it because he's basically a useless witness," Cramer said. "Cohen fell on his sword and has shown that he's a valuable cooperator. Manafort tried to play both sides and he got caught."

Trump, for his part, has defended Manafort extensively in recent days and praised his refusal to cooperate with Mueller. And experts say a presidential pardon may be Manafort's last hope after his plea deal fell through.

"He's like a guy at the casino table who's lost all his money at craps," Cramer said. "And now he heads to the ATM to try to turn things around. Donald Trump is basically the ATM."

Grace Panetta contributed reporting.