Counterintelligence investigators were reportedly considering whether Trump's actions constituted a national security threat, an extraordinary line of inquiry against a sitting USA president. Manafort allegedly lied to the Mueller investigation about all these actions.
It previously reported Mueller and the FBI are investigating Trump for possible obstruction of justice over Comey's firing, but the counterintelligence investigation into Trump had not been disclosed until the Times scoop.
Trump can continue to say that the Mueller probe is a hoax and a witch hunt.
"Agents and senior F.B.I. officials had grown suspicious of Mr. Trump's ties to Russian Federation during the 2016 campaign but held off on opening an investigation into him, the people said, in part because they were uncertain how to proceed with an inquiry of such sensitivity and magnitude".
Giuliani said the ball was now in the special counsel's court.
The counterintelligence investigation was ultimately opened after Trump publicly discussed Comey's firing, suggesting it was because of the Russian Federation probe.
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The inquiry is now part of special counsel Robert Mueller's broader investigation into the 2016 election and whether any of Trump's associates conspired with any Russian interference. "We weren't convinced they had any questions they don't know the answer to". Apparently, the bureau's knowledge of the Trump Tower meeting, and Trump's July 2016 press conference request - "Russia, if you're listening, I hope you're able to find the 30,000 emails that are missing - wasn't enough to pull the trigger on an inquiry".
"The investigation the F.B.I. opened into Mr. Trump also had a criminal aspect, which has always been publicly known: whether his firing of Mr. Comey constituted obstruction of justice".
Read the entire New York Times report here.
The lawyer, Michael Cohen, has been sentenced to three years in prison for multiple crimes, including felony violations of campaign finance laws he undertook, prosecutors alleged, under Trump's direction.
If the report is not made public, however, Congress could issue a subpoena to try to force its release.
Giuliani said it is unclear to the legal team whether acting Attorney General Matthew Whitaker or Deputy Attorney General Rod Rosenstein is now in charge of the investigation.