The New York Times reported on May 15, 2018, that Trump campaign policy aide and later White House Deputy Cabinet Secretary John Mashburn testified to the Senate Judiciary Committee in March 2018 that he recalled receiving an email from George Papadopoulos in the first half of 2016 indicating that the Russian government had damaging information about Hillary Clinton. Before this report, there had been no publicly available information indicating that Papadopoulos had informed anyone on the Trump campaign about such matters. Despite an extensive search for the purported email by various investigators, it has not been located. A court document Mueller's office filed in association with Papadopoulos's guilty plea included verbatim quotes from various emails Papadopoulos had sent or received, but the Mashburn email was not referenced in that document.
The New York Times reported on January 11, 2019, that FBI counterintelligence grew concerned about Trump's ties to Russia during the 2016 campaign but held off opening an investigation because of uncertainty about how to proceed on such a sensitive matter. Trump's behavior during the days immediately before and after Comey's firing caused them to begin investigating whether Trump had been working on behalf of Russia against U.S. interests, knowingly or unknowingly. The FBI merged that counterintelligence investigation with a criminal obstruction of justice investigation related to Comey's firing. Mueller took over that investigation upon his appointment, although it was not immediately clear if he had pursued the counterintelligence angle.
More InfoThe Steele dossier asserted that Trump attorney Michael Cohen in August 2016 had a clandestine meeting with Kremlin representatives in Prague. Cohen has stated he has never been to Prague, inviting investigators to examine his passport. McClatchy reported on April 13, 2018, that Mueller's investigators have evidence that in August or early September 2016 Cohen traveled to Prague by way of Germany. Such a trip would not have required a passport as Germany and the Czech Republic are in the Schengen Area which has abolished passport and all other types of border control at their mutual borders. On April 14, 2018, Cohen again denied he had ever been to Prague, although weeks after the 2016 election he had told journalist David Corn he had been in Prague fourteen years earlier. McClatchy reported in December 2018 that a mobile phone traced to Cohen had "pinged" cellphone towers around Prague in late summer 2016. McClatchy also reported that during that time an eastern European intelligence agency had intercepted communications between Russians, one of whom mentioned that Cohen was in Prague. The Mueller Report did not conclude Cohen had been in Prague, citing his testimony to investigators.
More InfoThe special counsel also took over an FBI investigation on whether President Trump had committed obstruction of justice, which began within eight days after Trump's dismissal of FBI Director James Comey. CNN reported in December 2018 that then-acting FBI Director Andrew McCabe started the investigation based on Comey's firing—which had been recommended in writing by Rosenstein in what became known as the Comey memo—and also Comey's allegation that Trump had asked him to stop investigating Trump's former national security adviser Michael Flynn. In February 2019, McCabe, since fired from the FBI, confirmed he launched the obstruction of justice investigation for those reasons, and gave additional reasons such as Trump's multiple depictions of the investigation into Trump associates and Russia as a "witch hunt", as well as Trump allegedly telling Deputy Attorney General Rod Rosenstein to mention the Russia probe in Rosenstein's memo to recommend firing Comey, and Trump's comments to the Russian ambassador and NBC relating Comey's firing to the Russia probe.
More InfoWhitaker, a vocal Trump supporter, had publicly criticized the Mueller investigation on several occasions before joining the Justice Department in September 2017, asserting it was "going too far" and referring to it as a "lynch mob". Whitaker is also a personal friend of Sam Clovis, a former co-chair of the Trump campaign who has testified to Mueller's investigators and grand jury. Because of his prior statements and involvement, many Democrats and some Republicans have asserted that Whitaker's potential conflicts of interest require him to recuse himself from overseeing Mueller, although Whitaker reportedly indicated he had no intention of doing so. Justice Department ethics officials typically review conflicts of interest to recommend recusals, but their findings are not binding and are usually kept confidential.
More InfoCNN reported on September 19, 2017, that Manafort had been a target of a FISA wiretap both before and after the 2016 election, extending into early 2017. Some of the intercepted communications caused concerns among investigators that Manafort had solicited assistance from Russians for the campaign, although the evidence was reportedly inconclusive. The wiretaps began sometime after Manafort became a subject of an FBI investigation into his business practices in 2014. The Mueller investigation was provided details of these intercepts.
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