Elie Honig, a former federal and state prosecutor, is a CNN legal analyst and a Rutgers University scholar. The views expressed in this commentary are his own. View more opinion articles on CNN.

(CNN) President Trump and his allies have long rallied around the defiant battle cry that special counsel Robert Mueller is conducting a " witch hun t" that has uncovered " no collusion " with Russia. But public filings by Mueller and the Southern District of New York over the past two weeks have changed the game. We still do not know everything Mueller knows, but the contours of a broad scheme by the administration to conspire with Russia -- to the personal benefit of Trump and the detriment of the United States -- are now coming into sharper focus.

Over the past two weeks, we have been reminded that Mueller knows more than anybody else, and he does not go out on limbs. If Mueller says it, then he knows it and can prove it. Friday's public filing on Paul Manafort's failed cooperation is a case in point. Manafort lied during the cooperation process, Mueller caught him, and (even based solely on the non-redacted portions of the memo) Mueller laid out the proof in methodical fashion before the court. Mueller doesn't bluff. If he raises, he's got the cards.

Even before the recent spate of court filings, Mueller had generated impressive results. He has indicted over 30 people, including teams of Russian social media manipulators and intelligence agency hackers , and he has convicted Trump's former campaign chair ( Manafort ), national security adviser ( Michael Flynn ), personal attorney ( Michael Cohen ) and other campaign advisers ( Rick Gates and George Papadopoulos ) of federal crimes. Even if Mueller's investigation had ended two weeks ago, it would have uncovered historically significant corruption at the highest levels of politics and government.

Now, with Mueller's recent court filings, the battleground ahead is coming into sharper focus. It now seems that Mueller is operating on two fronts, both of which pose deadly serious threats to Trump and his administration.

First, the evidence mounts that Trump has committed federal crimes unrelated to Russia. When Michael Cohen pleaded guilty in August to campaign finance violations based on hush money payments to Stephanie Clifford and Karen McDougal, he testified under oath that he had acted "in coordination and at the direction of" Trump. In his sentencing memo filed last week, Cohen reiterated that he committed the campaign finance crimes " in accordance with [Trump's] directives ." When Cohen pleaded guilty, White House Press Secretary Sarah Sanders said "the President in this matter has done nothing wrong, and there are no charges against him."

In Friday's filing , the SDNY writes that "with respect to both payments, [Cohen] acted in accordance with and at the direction of" Trump. That is a very big deal. It is one thing for Cohen unilaterally to claim Trump participated in a federal crime; it is another for the United States Department of Justice to confirm it. (Shortly after the public filing of the SDNY memo, Trump -- entirely inexplicably -- tweeted, "Totally clears the President. Thank you!")

Federal crimes of any variety are a big deal, and federal crimes committed by the President are monumental. An ordinary person in Trump's position would face potential criminal charges (though it is unlikely Mueller will indict a sitting president given current DOJ policy ). And the President's conduct raises serious questions about abuse of power that will play into any consideration of impeachment by the incoming Democratic House majority.

Second, it is increasingly clear that Trump had deep financial and political incentives to curry favor from Russia as the 2016 election approached. Mueller's recent filings have begun to answer the "why?" question: why did Trump want so badly to please Russia and why did Russia want to help him win the presidency?

Cohen's guilty plea last week , and the sentencing memos that followed , provide the clearest answer we have seen thus far. We now know that, as late as June 2016 -- well into the presidential campaign and after Trump had become the presumptive nominee -- the Trump Organization sought to build a tower in Moscow and needed approvals from the Russian government to make it happen.

Based on these revelations, we now know that Trump was compromised deep into his run for the White House. Trump needed to curry favor with the Russian government to obtain approvals for the Moscow project. Further complicating matters, while Trump lied to the public about his business dealings with Russia, the Russian government had proof to the contrary -- in the form of written communications with Cohen -- which Russia could have used for leverage over Trump.

Because of his own financial dealings and lies to the public, Trump gave Russia the ability to influence and potentially manipulate him. Given that, it's no wonder Russia tried to help Trump win the election, as Mueller has alleged in the indictment of Russian intelligence agency hackers

And there plainly is even more lurking beneath the surface of what Mueller has revealed to the public thus far. Most ominously, in Friday's sentencing submission for Cohen, Mueller writes that Cohen -- who, in Mueller's assessment was "credible and consistent with other evidence" -- provided Mueller with "useful information concerning discrete Russia-related matters core to [Mueller's] investigation that he obtained by virtue of his regular contact with [Trump Organization] executives during the campaign."

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The puzzle pieces fit together. Trump needed Russia for his business dealings. Russia wanted Trump to win because they could influence or control him. And the Trump team wanted Russian help simply because they thought the Russians could help Trump win the election. Everyone profits, everyone gets what they want.

All of that depended, of course, on the truth remaining hidden. Mueller already has exposed plenty of truth -- much of it in court filings these past two weeks -- and he has made clear that much more is to come. Soon even the staunchest Trump defender will not be able to argue credibly that Mueller has come up empty on his core mandate to investigate Russian interference in the 2016 election. It won't be long until "no collusion" is no more.