Early last month, as part of its effort to investigate Russian interference in the 2016 US presidential election, the FBI filed an affidavit in federal court explaining why the bureau wanted to keep secret a plea deal it had struck with a low-level former Trump campaign adviser named George Papadopoulos.

On the surface, the request seemed unusual. Mr. Papadopoulos was a bit player in the Trump 2016 effort, a young, unpaid foreign policy adviser who attended meetings but seemed to do little else. Why cloak the fact that Papadopoulos had lied to agents and then deleted social media accounts in a hapless attempt to conceal his actions?

But the FBI had its reasons, special agent Jennifer Zelski Edwards argued in the October affidavit. During 2016, Papadopoulos had had direct contact with Russian nationals and Russia-linked foreigners. Then he’d talked about these contacts with officials up and down the Trump campaign chain of command.

The FBI planned to interview these people, too – and the bureau did not want them to know that a former associate had flipped. In essence, Papadopoulos was a truth check, an informer who could help the bureau determine if any new interviewee was lying.

“The investigation is ongoing and includes pursuing leads from information provided by and related to the defendant regarding communications he had . . . with certain other individuals associated with the campaign,” Ms. Edwards wrote in the affidavit.

The investigation is ongoing, indeed. Six months after Robert Mueller’s appointment as Department of Justice Special Counsel in the Russia probe, it seems increasingly clear that his effort is akin to an attack submarine, large and potentially dangerous to its targets, moving most of the time stealthily, submerged beneath the waves.

On October 30 the investigation rose suddenly into full public view. Mr. Mueller’s team unsealed Papadopoulos’s guilty plea, and made public indictments against former Trump campaign manager Paul Manafort and associate Rick Gates alleging money laundering and other international crimes.

Now Washington awaits the investigation’s next surface appearance. What will it reveal?

What we may have learned so far, according to Norman L. Eisen, former White House Special Counsel for Ethics and Government Reform under President Obama, is that Mueller is investigating whether dots of contact between Trump officials and Russians are part of a chain of coordination, or isolated and unimportant. It’s also apparent that Mueller won’t shy away from filing charges against high officials for alleged offenses that may not have been directly related to campaign activities.

“Mueller will pursue the evidence where it leads. All you can really ask is that you have a qualified, fair, independent investigation,” says Mr. Eisen, who also served as Ambassador to the Czech Republic and is now a senior fellow in governance studies at the Brookings Institution.

Putin ‘means it’

For his part, President Trump made news over the weekend by seeming to accept Russian leader Vladimir Putin’s personal denial that Russia tried to tamper with the 2016 election. Mr. Putin’s assertion was sincere, Mr. Trump said on Saturday to reporters on Air Force One. “Every time he sees me, he says, ‘I didn’t do that,’” Trump told reporters. “And I believe – I really believe that when he tells me that, he means it.”

A day later, Trump dialed this back by saying: “I’m with our agencies.” US intelligence has concluded that Moscow did, in fact, try to meddle in the 2016 political process.

But the president continued to dismiss the Russia investigation as a Democratic “hit job,” and insisted that the US needs to move on from the probe and instead try to get Russian cooperation on Syria and other world problems.

“We have to get to work,” Trump said on Sunday.

Despite Trump’s wishes, Mueller’s investigation shows no sign of slowing down. Just the opposite.

Carolyn Kaster/AP Former National Security Adviser Michael Flynn is considered a likely target of the Mueller investigation.

It seems possible that the next big target in Mueller’s sight may be former National Security Adviser Michael T. Flynn. NBC News reported last week that the Russia probe has already amassed enough evidence to bring charges against Mr. Flynn for alleged infractions relating to his private lobbying and consulting work. As with Mr. Manafort and Mr. Gates, at issue might be concealment of foreign work and the laundering of foreign money.

Flynn in ‘a lot of trouble’

The Manafort charges are a “straight analogue” to some of Flynn’s alleged activities, says Andy Wright, an associate professor at Savannah Law School and a founding editor of the legal blog Just Security.

“Flynn is really in a lot of trouble,” Professor Wright says.

Flynn’s son, Michael Flynn Jr., might be in jeopardy as well. He served his father as a top aide and chief of staff during the time frame under scrutiny by Mueller’s team.

Whether prosecutors will actually move to indict either of the Flynns remains to be seen. It is possible that their real aim is to pressure the former national security adviser to cooperate in the larger Russia investigation.

Beginning before last year’s Nov. 8 election, and continuing through the transition period, Flynn had a number of communications with Russian Ambassador Sergey Kislyak. (He was later fired from the White House for allegedly misleading Vice President Mike Pence about these discussions.) What did Flynn and Mr. Kislyak talk about, and why? Who else in the president-elect’s circle knew they were in touch? Was Flynn directed to talk about the future course of sanctions or other important aspects of US-Russian relations?

Flynn could trade information about his Russia dealings for lighter treatment, as Papadopoulos appears to have done.

President Trump has long insisted that the Russia investigation is a “witch hunt” and that there was “no collusion” between his campaign and Russia.

Indeed, it is possible that the documented contacts between his campaign staff and Russians or Russia-linked foreigners were innocent, or happenstance. As an incoming top official, Flynn might well have wished to speak with the Russian ambassador, for instance.

Connections piling up

However, the number of connections with Russia is piling up. Besides those mentioned above, Donald Trump Jr. and Jared Kushner, along with Manafort, met with a Russian lawyer named Natalia Veselnitskaya and others at Trump Tower on June 9, 2016. Trump lawyer Michael Cohen corresponded with Russians about building a Trump Tower in Moscow through January of 2016.

Foreign policy adviser Carter Page gave a speech in Moscow critical of US foreign policy in July 2016. Attorney General Jeff Sessions has met Russian Ambassador Kislyak on several occasions. Campaign adviser J.D. Gordon and Mr. Page met Kislyak at a July 20 event associated with the Republican National Convention.

Whether there has been collusion or not between Russia and Team Trump may depend on the definition of “collusion.” If it means mutual cooperation to disseminate stolen Democratic emails or other activity, Trump might be correct to say no evidence has yet proved the case. But if it includes a willingness to engage in such activity, and to meet to talk about it, he is wrong, according to critics. And Mueller’s investigation is not over.

“There is a lot of evidence that is continuing to emerge . . . that points to collusion,” says Eisen of Brookings.

Mueller is likely interested in two particular incidents. One is the June 9 Trump Tower confab, at which Donald Trump Jr. expected to receive high level and sensitive information obtained by the Russian government that would be damaging to Hillary Clinton.

“If it’s what you say I love it,” the younger Trump wrote in an email prior to the meeting.

The outcome of the meeting remains unclear. Mr. Trump has said it was a waste of time and that Ms. Veselnitskaya provided no useful information. Veselnitskaya, for her part, said in an interview with Bloomberg News last week that Trump Jr. indicated that a law targeting Russia with sanctions could be re-written if his father won the election. He also asked for written evidence that the Clinton campaign had received illegal contributions.

The second incident centers on George Papadopoulos. In April 2016, Papadopoulos met with a Maltese professor with close ties to the Russian government, who told him that Moscow had “dirt” on Mrs. Clinton in the form of “thousands of emails,” according to a Statement of the Offense from Mueller’s office filed with a federal court on Oct. 5.

Who else did Papadopoulos tell about this “dirt?” How did they react to the information, and to Papadopoulos’s continued offers to try to set up a meeting with Russian leader Vladimir Putin and Trump himself?

This is where the story circles back to Mueller’s request to seal Papadopoulos’s guilty plea. It is likely that he wanted to hear what Gordon, Page, and other mid-level Trump campaign workers had to say about the matter, without them knowing that he had a second source of information – someone who had already pled guilty.

Thus it would not be surprising if Gordon or Page is integral to whatever public turn the investigation takes next.

A key footnote

There’s one further hint of how Mueller is trying to connect the dots of the investigation, contained in the fine print of recent court filings. It’s a footnote, in fact, from Papadopoulos’s plea deal.

Around May 21, 2016, Papadopoulos emailed a high-level Trump campaign official, reiterating that Russia wanted a Trump meeting. Press reports have identified the recipient of that email as newly named campaign chief Paul Manafort. Manafort then forwarded the email to a third party, identified in press reports as Rick Gates.

The footnote in the plea deal outlines what Manafort said to Gates about the offer of a Trump-Putin meeting. “Let’s discuss,” he said. “We need someone to communicate that DT is not doing these trips. It should be someone low level in the campaign so as not to send any signal.”

This is ambiguous. Does it mean that Manafort wanted to send someone low level to say that Trump wasn’t doing quasi-summit meetings yet? Or does it mean that he wanted someone low level to actually hold a meeting, presumably to discuss items of mutual interest?

This is also the context in which Manafort, Trump Jr., and Mr. Kushner held their Trump Tower meeting with a Russian lawyer on June 9.

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One thing seems clear: There will be more days like Oct. 30, when big news from the Mueller probe commanded Washington’s attention. If Trump reacts with the vehemence he has to this point, he may further erode his remaining power to get things accomplished as president, says Wright of Savannah Law School.

“Almost any of these news days are going to be not great days for the president," says Wright. "All of these types of stories will continue to burn down his candle of goodwill.”