In this process, the Special Adviser begins to reveal lies and blurring that people around Trumpa, the president himself, have raised to try to hide multiple, inexplicable connections with the Russians before and 2016.
He offers implicit explanations on the way for President's strangely happy relationship with Russian President Vladimir Putin.
And Mueller now crossed the red line Trump once warned he could boost his ignition – probing his business empire.
By sponsoring a court document describing Cohen's recognition and his team's 70 hours of extra testimony, Mueller signals that his new star witness might have more to say and that more serious discoveries may be made.
Thursday, in fact, was the most significant day in Mueller's probe that gave a long shadow over Trump's presidency.
The cooperation agreement could offer documents, other evidence and testimonies that could lead Mueller deep into Trump's family and personal circle.
Cohen's acknowledgment that he lied in Congress on Trump's attempt to conclude an agreement on the construction of the Trump Tower in Moscow, deep in the 2016 presidential campaign, raised tremendously worrying issues Mueller still needs to answer.
In fact, he told the story of a presidential candidate trapped in a commercial relationship with the people Mueller had accused in previous indictments for conducting "informative warfare" against the United States in order to disrupt the elections and help Trump set the White House.
"Two great questions about the image – is any person acting as a link between the campaign and Russia or WikiLeaks, and what was the incentive for Trump to work with the Russians and why he so much encouraged the Russians?" said Jens David Ohlin, deputy dean Cornell Law School.
"I think we now have potential answers to these questions."
What Mueller has not yet proved
Mueller has yet to prove that Trump's business activities have shedding light on Russia's approach. He did not directly contradict Trump's fierce denial of the agreement between his campaign and Moscow.
Furthermore, it is unknown whether Mueller has documented evidence that implies a president in any evil, or simply relies on Cohen's testimony. Many legal experts suspect that he would bet on a witness like Cohen, who admitted lying, without any supporting evidence.
But there are no clear indications that Trump violated the law. And, despite the events on Thursday, there is no indication that the political situation in Washington that still makes unlikely probabilities has changed.
Trump, just after landing in Buenos Aires for the G20, showed that the investigation is still in the mind despite the upcoming conference.
"This is an illegal Hoax that needs to be completed immediately," the president was tweeted late on Thursday.
But the event's development on Thursday must also be visible in the context of Mueller's work so far.
In a series of indictments, he has built a picture of a sophisticated Russian hacking operation, an attempt to insist on political media lying and distraction in American media, and indicts and condemns several Trump associates and advisors for lying on his investigation.
Now he could try to find Trump and his people well acquainted with Russian activity, despite their fierce assertions, there was no agreement.
Some observers believe that a rich detail in Mueller's legal submissions is one of the ways of painting a picture of Russian interference and the behavior of Trump's world if the president finds some way to block his eventual final report.
There are immediate and long-term political and legal consequences that Cohen throws firmly into Mueller's camp.
His allegations, under oath and with the certainty of long-term imprisonment, if untrue, directly contradict Trump's assurances that he had no business or business relationship with Russia.
If that was the case, Trump wisely lied to the American people.
In yet another shock, Cohen said he lied for political reasons.
"I made these statements to comply with the individual's political messages and to be loyal to Individual-1," Cohen said in a document filed with the court, referring to the president.
His statement raises another question that was not answered in the document.
Did the President know that Cohen was lying in Congress or forced him to do so? If he has done so, such a move will surely rise to the level of power abuses that would be part of all prosecution articles.
The president on Thursday condemned Cohen as "weak" and said he was lying to Mueller to release long-term prison sentences after admitting tax and financial fraud. He told reporters before he went to the G20 Summit in Argentina, in an unwelcome statement that showed his discomfort.
Trump's lawyer Rudy Giuliani also broke Cohen.
And he tried to ask a question around Washington immediately after Cohen's news: Did Trump tell a different story of his hope that he would build a Trump tower in Moscow in a written response from a special attorney to what Cohen testified, Mueller's version of the story clearly believes?
Giuliani said "there is no contradiction" between Trump's response to Mueller and Cohen. And he suggested that, waiting to move to Cohen until the president left for a few days, answering questions, he could set a trap.
"Their covertity did not succeed if that was what they were trying to do," Giuliani said.
Trump's defense could go back
Still, Trump's self-defense raised another question that would weaken his position and cause trouble for his legal team.
He said he was justified in seeking business opportunities in Russia as he ran for president because he could not reach the White House and therefore should not be punished by losing the opportunity to make money.
"It would not be a bad thing if I did it. I ran business while I was in the campaign," Trump told reporters.
"There was a good chance I would not win, in which case would I go back to work and why would I lose a lot of opportunities?"
Trump's comment left the impression that he used his platform as a presidential candidate as a means of enriching himself instead of serving the American people.
More worryingly, the ability to seek favorable treatment from Russia could offer a motivation for change that caused hostile attitude towards Russia on the Platform of the Republican National Convention.
The fact that he was lying to have no business ties with Russia after the implementation of the agreement offered Moscow to use it when it became president, opening up the possibility of serious threat to national security if considered to be compromised.
Trump could also undermine a possible defensive path, that Cohen was the primary actor in search of Trump Tower in Moscow when he said, "I decided not to make a project, so I did not do it."
Some Trump fans have warned of irresponsible jumping on the conclusions and question Cohen's credibility.
"Heaven drops suddenly because there is another plea agreement," said Jim Schultz, a former White House Trump attorney at "Cuomo Prime Time".
The White House had been raised for a Cohen bomb since appearing in Washington to meet Mueller's prosecutors earlier this month.
What matters most is worrisome, and other people close to Trump, who might be involved with the Russian organization, are what he said in the consultations that were extending for three full days.
Pamela Brown contributed to this report.