After President Donald Trump’s former Campaign Chair Paul Manafort was found guilty on 8 counts of federal criminal charges brought by Special Counsel Robert Mueller, he decided to try his luck and avoid a second trial by becoming a cooperating witness in the Russia investigation. It didn’t work out — in November 2018, Mueller’s team revealed that they believed Manafort was lying about key facts in their interviews, nullifying his cooperation deal.

Since then, details about his alleged lies have slowly emerged in various court documents. And a new transcript of closed-door hearing in the case released Thursday exposed stunning new details about the Mueller team’s thinking and its progress in the investigation.

Despite reports that Mueller’s investigation is going to be wrapping up soon, the transcript suggests that, at least recently, the special counsel was still pursuing key parts of its mission in the Russia investigation. And though he isn’t mentioned by name, the transcript contained a particularly revealing detail about the president with damning implications.

While many conservative critics of the investigation — most notably Trump — have dismissed the idea that there was any “collusion,” criminal or otherwise, between the campaign and Russia’s efforts to interfere in the election, the special counsel’s office made clear in the hearing that it is still interested in these questions. Discussing the importance Manafort’s lying about his contacts with Konstantin Kilimnik, a Russian political consultant, prosecutor Andrew Weissman said:

So, I mean, this goes to the larger view of what we think is going on, and what we think the motive here is.

This goes, I think, very much to the heart of what the special counsel’s office is investigating. And in 2016. there is an in-person meeting with someone who the government has certainly proffered to this court in the past, is understood by the FBI, assessed to be — have a relationship with Russian intelligence, that there is [redacted]. And there is an in-person meeting at an unusual time for somebody who is the campaign chairman to be spending time, and to be doing it in person.

The meeting and what happened at the meeting is of significance to the special counsel.

To make explicit what the special counsel’s office is saying here: Manafort’s meeting with a man with ties to Russian intelligence during the heat of the 2018 campaign is at “the heart” of the Russia investigation. The meeting is important to the special counsel. And the special counsel thinks that these facts give Manafort a motive to lie about it — suggesting he’s covering up incriminating behavior.

A previous court filing revealed that in one of his meetings with Kilimnick, Manafort provided him with polling data, indicating the meeting was directly related to the election.

And even The Daily Caller’s Chuck Ross, a frequent critic of the Russia investigation, pointed out Thursday that the meeting with Kilimnick Weissman referenced was on Aug. 2 — a month after Manafort sent a Kilimnick an email offering private briefings to Russian Oligarch Oleg Deripaska, to whom Manafort was reportedly in debt.

The above section of the transcript is followed by significant redactions, suggesting sensitive material that the government still wants secret lies beneath. And Weissman was also careful to note to the judge that there were certain facts he wasn’t willing to reveal in court.

At another point in the transcript, a prosecutor tells the judge that one of Manafort’s motives for lying to investigators about something he told to Rick Gates, another former Trump aide who is cooperating in the probe,  was that he was trying to “augment his chances for a pardon.” (NBC News noted that the transcript appears to incorrectly attribute this remark to one of Manafort’s lawyers, when it is, in fact, clearly a prosecutor speaking.)

This is the first time the special counsel has indicated publicly that it thinks a witness or target in the investigation might be angling for a pardon. Many have speculated that the pursuit of a pardon could explain Manafort’s otherwise puzzling behavior.

But since a pardon for federal crimes could only come from the president, the special counsel’s acknowledge of this possible motive is remarkable. It means the special counsel believes Manafort could increase his chances of a pardon by with a criminal lie. This, quite directly, implies that Trump has an interest in one of his former aides engaging in a criminal cover-up — a circumstance that is hard to imagine unless the president himself is at least indirectly implicated in criminal behavior.

While many have long suspected and argued as much, it is still a stunning turn of events to have it confirmed by prosecutors in court.

Legal analyst Luppe Luppen speculated on Twitter that, in a redacted portion of the transcript, prosecutors may have listed the possibility of a presidential pardon as an “unusual factor” in Manafort’s plea agreement.

The transcript also reveals that Manafort met with Kilimnik at Trump’s January 2017 inauguration, which is reportedly under investigation separately by the Southern District of New York. There, they discussed the promotion of a Ukraine peace plan, prosecutors said, which is believed to favor Russian interests. This shows that, despite Trump’s attempt to distance himself from Manafort after firing him in August of 2016, Manafort at least believed he had the chance to promote a political agenda under the Trump administration.

Other portions of the hearing also referred to connections between Manafort and the president since the inauguration. Prosecutor Greg Andres said that Manafort “constantly either minimizes the information he has about the administration or contact with the administration.”

He adds: “So there’s an issue whether or not during cooperation he’s communicating with [redacted] or perhaps providing information about questions or other things that are happening in the special counsel investigation, whether’s he’s sharing that with other people.”

After Manafort had agreed to cooperate, Rudy Giuliani, the president’s lawyer, revealed that the ex-campaign chair had stayed in his joint defense agreement with the president, a situation legal experts said was extraordinary and posed the risk that he could innappropriately share sensitive information.

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