WASHINGTON — In the weeks after Donald Trump became the Republican nominee in late July 2016, the FBI warned him that foreign adversaries, including Russia, would attempt to spy on and infiltrate his campaign.

It was a standard briefing, the kind routinely given to presidential candidates, capped with an admonition that Trump should call the FBI if he learned of any unusual approaches from foreigners.

But there was something the FBI didn't tell him.

The bureau just recently had opened counterintelligence investigations into four Trump advisers suspected of improper interactions with Russians — a fact, then-secret, that emerged much later in Congressional testimony.

Two of the four, Paul Manafort and Michael Flynn, were top Trump aides with Russian baggage. A third, George Papadopoulos, had been offered Hillary Clinton emails by a Russian agent. The fourth, Carter Page, had traveled to Russia while advising the Trump campaign.

Those FBI inquiries grew into what has become special counsel Robert Mueller's sprawling Russia investigation — a legal juggernaut that threatens to overwhelm Trump's presidency.

The Mueller probe has led to criminal charges against 33 people, including three of those original four, and engulfed the Trump administration in a legal and political morass unlike anything the country has witnessed since the impeachment of President Bill Clinton, and before that, Watergate.

But a central question remains unanswered, and it's one that could hold the key to what happens over the next few months: What did FBI officials know in the summer of 2016 that dissuaded them from telling Trump they were investigating his top aides?

The world may soon know the answer. Government officials and others familiar with the situation tell NBC News that Mueller is nearing the end stages of his investigation, and a report by the special counsel is expected to be submitted to the Justice Department as early as mid-February.

Appointed in May 2017, Mueller, a Republican, Vietnam combat veteran and career public servant who led the FBI after 9/11, assembled a team of veteran prosecutors. They called upon the fruits of secret U.S. intelligence gathering to lay bare, in two indictments, how Russian intelligence officers and agents used fake social media personas and illegal hacking to hurt Hillary Clinton and help Donald Trump.

When it comes to any American involvement in that Russian operation, much of what Mueller has learned remains a tantalizing secret.

Even so, the evidence that has surfaced so far — of crimes and lies and questionable judgment — is of a sort that might have crippled previous presidencies.

Court documents, emails and testimony have shown that the president's son was willing to accept incriminating information on Clinton from the Russian government; that the president didn't tell the truth about his dealings with Russia during the campaign; and, in a separate federal probe, that the president directed his lawyer to commit campaign finance crimes.

Three men who once sat in Trump's inner sanctum — Michael Cohen, Paul Manafort and Mike Flynn — have been convicted or pleaded guilty to serious crimes and have cooperated, to varying degrees, with the investigation.

A number of the assertions in the controversial Steele dossier on Trump, paid for by Democrats and compiled by a former British spy — though they are raw, uncorroborated and derided by Trump and his allies — have proven to be accurate, according to multiple analyses by former intelligence officers.

But.

And it's an important "but."

Mueller has so far not showed the public proof that speaks to the central question he was hired to answer: Whether Trump or any of his associates actively conspired with the effort by Russian intelligence officers to hack, leak and otherwise interfere in the 2016 election. None of the criminal charges filed to date have addressed that issue.

That stubborn fact, which could change any day or remain fixed for eternity, is what fuels Trump allies who echo the president's assertion that the investigation is illegitimate.

On Sunday, Trump lawyer Rudolph Giuliani challenged Mueller via Twitter to "put up or shut up. You have no evidence of the President being involved in a conspiracy with anyone including Russia ... And you also have no evidence of collusion."

I challenge Mueller to put up or shut up. You have no evidence of the President being involved in a conspiracy with anyone including Russia to hack. And you also have no evidence of collusion. It’s been 2 years so submit a report to DOJ and we will answer it. — Rudy Giuliani (@RudyGiuliani) December 30, 2018

It's a view that is repeated daily in conservative media and embraced by tens of millions of Americans who remain loyal to the president.

"Collusion just does not exist," said Victoria Toensing, a conservative lawyer who represented Trump aide Sam Clovis and other unnamed witnesses in the probe, and therefore has been in meetings with the Mueller team.

"All these little things about a meeting with a Russian here or there," Toensing told NBC News. "It doesn't add up to anything."

Toensing said she believes the investigation was concocted by a cabal of government insiders "who decided they had to save the country from Donald Trump."

Many legal experts have a sharply different view.

They argue that what Mueller has already established is damning, and hints at far more shocking revelations to come.

"We have yet to see the smoking gun, but we have a lot of smoke," said Frank Figliuzzi, who once hunted for Russian spies as head of the FBI's counterintelligence division and is now an NBC News analyst. "Would I expect Mueller to have shown his hand yet in all of this? Absolutely not."

Trump's Twitter campaign to discredit Mueller has harmed the prosecutor's image among a subset of Americans, polls show. But among the public at large, it does not appear to be working.

Fifty-four percent of Americans believe Mueller has conducted a "fair investigation," according to an NPR/PBS News Hour/Maris poll this month, while 33 percent call it a "witch hunt."

In an NBC News/Wall Street Journal poll released Dec. 16, 62 percent of Americans say Trump has been untruthful about the Russia probe, while half of the country says the investigation has given them doubts about Trump's presidency

The Mueller investigation has already exposed serious misconduct, according to NBC News analyst Chuck Rosenberg, a former federal prosecutor who once headed the Drug Enforcement Administration.

"The president is all but an unindicted co-conspirator in election law crimes and Russia seems to crop up in every aspect of the case, from internet troll farms to GRU hacking to Manafort's business dealings. And all the false statements by Papadopoulos, Cohen, Flynn — all those cases concern Russia," Rosenberg said.

Daniel Goldman, a former federal prosecutor in New York, said he is beginning to believe that conspiracy with Russian election interference is not the most serious crime Mueller is investigating.

Goldman, also now an NBC News analyst, postulates that at the heart of the inquiry is a question of whether the president has made foreign policy decisions — particularly with regard to Russia and Saudi Arabia — for personal financial reasons, rather than in the best interest of the country.

"What we are learning is that there may have been a much larger conspiracy to provide sanctions relief to Russia either in return for personal business and financial benefits or in return for assistance in the campaign," Goldman said.

That is why, Rosenberg, Goldman and other legal experts say, the Mueller team almost certainly has obtained many years of Trump's tax returns and business records, and is poring over past transactions, particularly his foreign ones.

So it has come to pass that Trump is the first president in 40 years to withhold his tax returns from the public, but also the first president to have them scrutinized, in all likelihood, by a team of IRS and FBI experts.

Meanwhile, the question of whether Trump obstructed justice — by asking FBI Director James Comey to drop the bureau's investigation into Flynn, firing him when he didn't and publicly denouncing the investigation on Twitter — remains another subject of Mueller's inquiries, as an FBI lawyer recently confirmed to Congress.

The beginning

It started — at least one strand of it — at a bar in London.

In May 2016, George Papadopoulos, a young political striver who had landed a spot advising the Trump campaign on foreign policy, sat down for drinks with a senior Australian diplomat.

As the diplomat, Alexander Downer, later recounted it, Papadopoulos told him he had been informed by a mysterious Maltese professor that the Russians had thousands of emails that could embarrass Trump's opponent, Democrat Hillary Clinton.

At the time, few people were aware that the Russians had hacked the Democrats.

Two months later, when Democratic emails began leaking, Downer's report about his conversation with Papadopoulos reached the FBI, according to documents later released by Congress.

A photo from Donald Trump's Instagram account shows George Papadopoulos, third from left, at a "National Security Meeting" in Washington in March 2016. @realdonaldtrump / via Instagram

It was one of a number of troubling reports streaming into U.S. intelligence agencies that summer suggesting a covert Russian intelligence campaign to influence the upcoming U.S. election, current and former U.S. officials told NBC News.

Intelligence on what the Russians were up to was pouring in from allies, assets and electronic intercepts.

To their distress, FBI and CIA officials began to see indications that Americans might be helping.

John Brennan, who was the CIA director at the time, told Congress last year that he "encountered and am aware of information and intelligence that revealed contacts and interactions between Russian officials and U.S. persons involved in the Trump campaign."

He said he shared the CIA's intelligence with FBI Director Comey, who shared with him some things the FBI had learned.

On July 29, 2016, the bureau formally opened a counterintelligence investigation focusing on four people, according to congressional testimony by Comey.

U.S. officials told NBC News that the four people were Papadopoulos, Page, Manafort and Flynn.

Carter Page arrives on the same day as a hearing regarding Michael Cohen at the U.S. District Court for the Southern District of New York in Manhattan on April 16, 2018. Drew Angerer / Getty Images file

Page and Manafort had already been on the FBI's radar — Page because he had been previously targeted for recruitment by Russian intelligence; Manafort because of his consulting work for a Russian-backed Ukrainian politician.

It's not known exactly what got the FBI interested in Flynn, the former head of the Defense Intelligence Agency. One factor, officials said, was his decision to accept $45,000 to speak at the 10th anniversary gala of the Russian state media company RT in December 2015, where he dined with Russian President Vladimir Putin.

When the FBI briefed Trump on foreign spy threats after the Republican National Convention, it was decided that briefers would not mention that two of his top aides were under scrutiny, a former senior official told NBC News. The concern was that doing so could tip off the targets of the probe. Nobody knew what Trump would do.

"It really complicated matters tremendously given the nature of the individuals under investigation," the former official said.