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."

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.

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.

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.

COMEY OUT, MUELLER IN

As one of his last acts in office, President Barack Obama expelled 35 Russian diplomats and seized two Russian-owned compounds in the U.S. in response to Russia's election interference. Most experts expected Putin to respond in kind.

To their surprise, he took no action.

On Jan. 12, 2017, a possible reason for that emerged. Washington Post columnist David Ignatius reported that Flynn had been in touch with the Russian ambassador in Washington, Sergei Kislyak, several times on the day the expulsions were announced.

Flynn publicly denied the two men had discussed sanctions. Then he denied it to two FBI agents who came to interview him on Jan. 24.

What happened next set off a chain of events that led to the legal imbroglio in which Trump now finds himself.

Trump fired Flynn after it became clear he had lied to the vice president about his conversations with Kislyak. A day later, by Comey's telling, Trump pulled the FBI director aside in the Oval Office and asked him to drop the investigation into Flynn.

Three months later Trump fired Comey, citing a memo by Deputy Attorney General Rod Rosenstein criticizing Comey's handling of the Hillary Clinton email investigation.

The sacking shocked official Washington, conjuring up images of 1973's Saturday Night Massacre, when Richard Nixon ordered the removal of the Watergate special prosecutor. The rule of law seemed under threat, and Rosenstein's reputation as a straight-shooting career civil servant was in danger.

Rosenstein, who was in charge of the Russian investigation in the wake of a recusal by Attorney General Jeff Sessions, was stung by intense criticism. He decided he had to act.

What he did next changed Donald Trump's presidency.

Without consulting the White House, Rosenstein announced the appointment of Robert Swan Mueller III as special counsel in charge of the Russia investigation.

While Mueller reported to the Justice Department, his status as a special counsel immediately transformed the Russia investigation.

He had a separate budget and was able to pick his own team of prosecutors and agents, some of whom left jobs with seven-figure salaries. Unlike other federal law enforcement officers, they had the luxury of devoting every waking hour to a single assignment.

Their mandate seemed to be narrow: To investigate how the Russians interfered with the 2016 election, including whether Trump or his associates conspired with Russia. But the instruction also allowed Mueller to look into any other matters that arose.

Soon enough, other matters did arise.

In June, based on interviews Mueller's team was conducting with Cabinet members and others, it became clear that the special counsel was investigating the question of whether Trump had obstructed justice.

If the president wasn't under investigation before, he was now.

In July, FBI agents raided Manafort's Alexandria, Virginia, apartment, a sign that they had amassed significant evidence against him.

In October, Manafort and the second-in-command at his political consultancy, Rick Gates, were indicted on a host of bank and tax fraud charges related to their work for Russian interests in Ukraine. It was clear to most legal observers that Mueller was throwing the book at the former Trump insiders in part to secure their cooperation. It would only be the beginning of their legal troubles.

On the same day, Papadopoulos was charged with lying to the FBI about his contacts with the Maltese professor — a suspected Russian agent who told him about the Clinton emails.

That was the first indication that the Russians had broached the subject of hacked emails with a member of the Trump campaign. It remains unclear how far within the campaign that information traveled — another important unanswered question about Trump and Russia.

In December, Flynn pleaded guilty to lying to the FBI and agreed to cooperate with Mueller. Much of what he has told the special counsel — including why he lied about his conversations with the Russian ambassador — remains a mystery.

MUELLER INDICTS RUSSIANS, FLIPS TRUMP INSIDERS

Having slapped the cuffs on some of Trump's closest aides, Mueller and his investigators had come to preoccupy not only a president quick to vent his anger on Twitter, but much of the news-consuming public. The investigation hovered over Washington like a mysterious alien spacecraft that occasionally hurled energy bolts to set the capital abuzz.

Mueller's team was believed not to leak, and the only thing his spokesman would tell reporters on background is that more than half of the news reports about the investigation were wrong.

Still, reports of witnesses being summoned to visit with Mueller prosecutors — or angles Mueller was said to be investigating became a staple of Washington journalism throughout 2018.

Interesting strands seem to surface and then fade from view. A meeting in the Seychelles, a reported subpoena to a German bank, allegations of foreign campaign contributions — no one outside of Mueller's team had any clear idea where these stories fit, if at all, in the investigation.

For his part, Mueller spoke only through court documents. In February and again in June, he spoke loudly and in great detail, releasing massive indictments against Russians that harnessed the fruits of secret U.S. intelligence collection to expose how the Russian government and their agents manipulated the American electorate.

Read more at NBC.com.