Over 448 pages, special counsel Robert Mueller’s final report covered a huge amount of ground, from Trump campaign contacts with Russian operatives to President Donald Trump’s efforts to thwart Mueller’s probe.

But while Mueller found that the Trump campaign did not conspire with the Russian government, he didn’t resolve every mystery surrounding the Kremlin’s 2016 election interference scheme.

Story Continued Below

Several lines of inquiry that Mueller and the FBI — not to mention countless journalists and amateur Internet sleuths — had reportedly been pursuing went unaddressed in the copious document. They include mysterious interactions between the Trump Organization and Alfa Bank computer servers; the inner workings of the data mining firm Cambridge Analytica; and influence-peddling by Middle Eastern countries targeting Trump’s fledgling administration. Other avenues, like whether compromising tapes exist of the president and what a Russian oligarch did with the internal Trump campaign polling data he was given, were left open-ended.

It’s possible that some or all of these topics are being examined by federal prosecutors independent of Mueller’s office. Mueller revealed in his report that foreign intelligence and counterintelligence information was often transferred to FBI headquarters or field offices. Mueller also made 14 criminal referrals to the Justice Department and bureau. Only two of those referrals — involving Trump’s former personal lawyer Michael Cohen and former Obama White House counsel Greg Craig — are publicly known.

It seems clear that none of those subplots prompted Mueller’s team to consider bringing criminal charges. But while Mueller’s original mandate directed him to pursue both a counterintelligence investigation and a criminal probe, his report contains no classified information, leaving unknown to the public anything he might have discovered in that category.

Here are five of the biggest unresolved subplots of the Russia investigation:

Did a secret computer link exist between the Trump Organization and Moscow’s Alfa Bank?

Even before Mueller was appointed, the FBI was examining why a computer server for Alfa Bank, Russia’s largest commercial bank — led by oligarchs with close ties to Russian President Vladimir Putin — had thousands of contacts with a server used by the Trump Organization between May and September of 2016. A Slate report on the contacts based on research by computer scientists caused an online sensation just days before the election, until the New York Times reported that the FBI had concluded there could be what the paper called an “innocuous explanation” for the activity, like a marketing email or spam.

Many independent cybersecurity researchers and experts, many of whom worked at senior levels in the Pentagon, White House, and intelligence community, have continued to insist that the timing and frequency of the server activity was not consistent with an automated process. “The timing of the communication was not random, and it wasn’t regular-periodic,” one researcher told told the New Yorker last October. “It was a better match for human activity.”

Innocuous or not, the server activity is not addressed in the Mueller report at all. The only discussion of Alfa Bank comes within the context of efforts by its CEO, Petr Aven, to connect with the Trump transition team in December 2016. Those efforts were apparently unsuccessful, according to Mueller, which may have led the special counsel’s office to dismiss the computer server activity as inconsequential. But there’s still no conclusive explanation for the pinging, or why the Trump domain that Alfa was contacting abruptly disappeared two days after the New York Times notified Alfa’s representatives in Washington of the server activity.

Did Cambridge Analytica have ties to Russia or WikiLeaks?

One of the biggest subplots of the investigations into Russian election interference is the role the data mining firm Cambridge Analytica. But the controversial company didn’t appear once in the report, despite indications that Mueller had questioned and subpoenaed former employees.

The Trump campaign hired Cambridge Analytica in the summer of 2016, and it played a key role in trying to sway voters using pilfered Facebook data during the election.

Aleksandr Kogan, a Russian-American who worked at the University of Cambridge, helped the firm harvest the raw data of up to 87 million Facebook profiles beginning in 2014, which the company then used to micro-target political ads. There’s a WikiLeaks connection, too: Alexander Nix, the company’s CEO, has acknowledged reaching out to Assange in the summer of 2016 to offer his help in organizing any Hillary Clinton-related emails WikiLeaks planned to release.

Mueller subpoenaed Brittany Kaiser, the former business development director for the firm, earlier this year. She told The Guardian that she was fully cooperating. Sam Patten, a Washington-based operative who began cooperating with Mueller’s probe last year after pleading guilty to an unrelated charge, worked at the Oregon office of Cambridge Analytica’s parent company, SCL Group, in runup to the 2014 midterm elections. And Mueller quizzed several digital experts who worked on Trump’s campaign about the big-data firm, according to ABC.

Like the NRA, however, Cambridge Analytica is not mentioned at all in Mueller’s report. As such, it is still unclear what, if anything, the company knew about WikiLeaks’ plans or whether its micro-targeting efforts were coordinated with the Russian’s information warfare campaign.

Intriguingly, though, much of the portion of Mueller’s report dealing with Russia’s Internet Research Agency — which tasked internet “trolls” with spreading disinformation and propaganda during the election — was redacted in the final report because of potential harm to ongoing investigations.

What was the NRA’s relationship with the Trump campaign, and with Russia?

Since the election, there have been numerous but vague data points indicating the Russians might be trying to infiltrate the National Rifle Association as a way to connect with Republicans and Trump’s campaign.

Mueller’s report, however, failed to shed any light on the subject, despite media reports that the special counsel was poking around on the subject.

The first indication of Mueller’s interest in the potential ties came earlier this year, when former Trump campaign adviser Sam Nunberg told CNN the special counsel’s team had asked him about the campaign’s relationship with the NRA and the circumstances of a Trump speech there in 2015. The investigators continued asking witnesses about the campaign’s ties to the NRA as recently as December 2018, according to CNN.

And last July’s indictment of Maria Butina, a Russian national who sought to infiltrate both the Trump campaign and the NRA during the election, also raised questions about the group’s status as a potential intermediary between Trump and the Russians. Butina was charged with acting as an agent of a foreign government without notifying the Justice Department.

Butina was the first person to ask Trump in public about his position on Russian sanctions during a 2015 event in Las Vegas, and tried to broker a meeting between Trump and her Russian handler, Alexander Torshin, at an NRA convention in May 2016.

McClatchy later reported that FBI counterintelligence investigators were investigating whether Torshin laundered money from Russia into the NRA to help fund Trump’s campaign — the NRA spent $30 million to support Trump in 2016, triple what it spent on supporting Mitt Romney in 2012.

Despite the investigators’ interest, however, the gun-rights group was not mentioned a single time in Mueller’s report. And her case was handled by prosecutors in Washington, D.C., not by Mueller’s team.

What did WikiLeaks know about the source of the stolen emails?

Mueller did answer one lingering question about Russian election hacking — how Kremlin agents got their digitally pilfered emails to WikiLeaks.

But he didn’t address the more potentially damning question: Did WikiLeaks know it was getting the material from Russian cutouts?

In his report, Mueller outlines in detail how Russia’s military intelligence agency, the GRU, hacked Democrats during the campaign. Between March and April of 2016, the report says, “the GRU stole hundreds of thousands of documents from the compromised email accounts and networks” and disseminated them both through GRU agents posing as independent hackers — including “Guccifer 2.0” and DCLeaks.com — and WikiLeaks.

According to Mueller’s report, the GRU used those fake online personas to shuttle some of their stolen cache to WikiLeaks. Through DCLeaks, the GRU initiated a conversation with WikiLeaks about transferring stolen documents on June 16, 2016. Eight days later, WikiLeaks reached out to Guccifer 2.0 via Twitter and asked for “any new material.”

Mueller noted that Assange and WikiLeaks tried to obscure the source of the hacked materials by claiming in public statements that the DNC hack was an “inside job” carried out by Seth Rich, a murdered committee staffer, rather than by Russia.

But the special counsel’s office either wouldn’t or couldn’t explain what WikiLeaks knew about the true identity of the hackers.

“Both the GRU and WikiLeaks sought to hide their communications, which has limited the Office’s ability to collect all of the communications between them,” the report says, pointing to their use of encryption.

That information could be relevant to determining whether WikiLeaks acted in a journalistic capacity, as its founder Julian Assange has maintained, or as a “non-state hostile intelligence service” abetted by Russia, as then-CIA Director Mike Pompeo claimed in April 2017.

Assange was arrested in London earlier this month after Ecuador withdrew his asylum. He faces U.S. criminal charges for allegedly trying to help former U.S. intelligence analyst Chelsea Manning crack into a computer storing sensitive government files in 2010.

What about the infamous video tape alleged in the Steeele dossier?

Perhaps no element of the Trump-Russia scandal was as sensational as the claim, contained in an unverified dossier assembled during the campaign by former British spy Christopher Steele, that the Russians had kompromat on Trump in the former of video capturing him cavorting with prostitutes in a Moscow hotel room.

Although the alleged tape consumed vast public attention over the past two years, Mueller mentions it only briefly. His report states that Russian businessman Giorgi Rtskhiladze texted Michael Cohen on October 30, 2016 and said: “Stopped flow of tapes from Russia but not sure if there’s anything else. Just so you know …. ” Rtskhiladze told investigators that “tapes” referred to derogatory tapes of Trump rumored to be in the possession of the Agalarovs—a Russian-Azerbaijani family that hosted the Miss Universe pageant in Moscow in 2013.

Rtskhiladze told Mueller that he believed the tapes were fake. But for whatever reason, he didn’t tell that to Cohen, according to the report. Mueller does not draw a conclusion one way or the other. It remains unclear who might have been creating or disseminating such tapes, what their motive might have been — and whether anyone on Mueller’s team ever saw one or more of them.

The Trump campaign has hired its own in-house attorney for its 2020 reelection bid — shifting future business away from Jones Day, the law firm, that has represented Trump since his first run for president.

Campaign officials and advisers cast the decision to hire Nathan Groth — a former lawyer for the Republican National Committee and Wisconsin Gov. Scott Walker — as a money-saving move, supported by the businessman-turned-president who loves to cut costs.

Story Continued Below

But close Trump advisers say the decision also stems from disappointment with the White House’s former top attorney and current Jones Day partner, Don McGahn, whose behavior has irked the president and some of his family members.

Taking business away from Jones Day is payback, these advisers say, for McGahn’s soured relationship with the Trump family and a handful articles in high-profile newspapers that the family blames, unfairly or not, on the former White House counsel.

“Why in the world would you want to put your enemy on the payroll?” said one adviser close to the White House. “They do not want to reward his firm. Trump arrived at that point long ago, but the security clearance memo stories put a fine point on it.”

One February 2019 story, in particular, caught the White House’s attention, when The New York Times reported that the president ordered John Kelly, his chief of staff at the time, to grant a security clearance to Jared Kushner. Kelly had written an internal memo on it, according to the Times. That fact was closely held inside the White House, and few officials other than Kelly and McGahn knew, say two close White House advisers — and the administration blamed McGahn for the leak.

McGahn did not respond to an emailed request for comment. Trump campaign spokespeople did not immediately respond to a request for comment.

The Mueller report, released on Thursday, seems only to have fueled Trump’s anger. It portrayed McGahn as one of the key officials who stopped Trump from taking actions that might be deemed to have obstructed justice.

In one especially colorful passage, McGahn is quoted as saying that the president had asked him to do “crazy shit.” In another, Trump berates his White House counsel for taking too many notes, comparing him unfavorably to his longtime consigilere, the late Roy Cohn.

On Friday, Trump seemed to take aim at McGahn on Twitter, writing, “Watch out for people that take so-called ‘notes,’ when the notes never existed until needed.”

The decision to shift law firms has been in the works for weeks, however, and predates release of the Mueller report.

The loss of Trump campaign business will be a financial blow to the D.C. political law practice of Jones Day, which had raked in $5.5 million in legal fees since the start of the 2016 Trump campaign, according to data from the Federal Election Commission.

The campaign still intends to lean on Jones Day for litigation already underway, so it is not severing all ties, and as a global law firm with 43 offices and 2,500 lawyers, its work for Trump campaign is just one small piece of its business.

The current head of the Jones Day political law practice, Ben Ginsberg, did not respond to requests for comment on Friday.

Groth will report to senior lawyers on the campaign, according to a Republican operative familiar with the operation. He will handle all of the compliance work such as conventions, ballot access and run-of-the-mill services like reviewing employment contracts and leases. This was a more typical arrangement for a campaign, the operative added — to have an in-house attorney and then other outside law firms for additional help. In 2016, the Trump campaign leaned entirely on Jones Day and McGahn, a former appointee to the Federal Elections Commission.

The move marks the waning of a symbiotic relationship between the law firm and the sitting president. After McGahn was named White House counsel, he brought with him into the administration 12 Jones Day attorneys who worked in the counsel’s office, and the departments of Commerce, Agriculture and Justice, including the current solicitor general, who is responsible for arguing the administration’s positions before the Supreme Court.

At the time, David Lat of the legal blog Above the Law wrote: “This is very good news for Jones Day and the lawyers remaining at the firm. It’s great for the firm’s prestige, and it also means that JD lawyers will be eagerly sought after by clients with issues pending before their former colleagues.”

McGahn returned to Jones Day as a partner this March, leading the government regulation practice. McGahn, a close ally of Senate Majority Leader Mitch McConnell, continues to advise Senate Republicans on judicial nominations, while focusing his law practice on the nuances of regulation, another of his passions from his White House tenure. Allies say he doesn’t mind losing the Trump campaign work and is quite happy with his new setup.

Prior to joining the White House, McGahn worked as a partner in the election law group at Jones Day from June 2014 to January 2017.

Maggie Severns contributed to this report.