In May 2005, James B. Comey, then the deputy attorney general of the United States, stood before a select audience at the National Security Agency in Ft. Meade, Maryland. Fourteen months before, Comey had had a face-to-face confrontation with President George W. Bush at the White House, arguing that an NSA program of spying on Americans in the name of counterterrorism had bent the Constitution to the breaking point.

FBI Director James Comey attends a meeting with U.S. Attorney General Jeff Sessions at the Justice Department in Washington, U.S., February 9, 2017. REUTERS/Yuri Gripas

Comey had said “no” to the commander-in-chief. The Justice Department would not re-authorize the program. He was prepared to resign, and to take the then-director of the Federal Bureau of Investigation with him, which would have imperiled the Bush administration in an election year. That confrontation was a very deep secret. It stayed secret for two years after Comey’s NSA speech.

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"It can be very, very hard to be a conscientious attorney working in the intelligence community," he said to the NSA officers. "Hard because we are likely to hear the words: 'If we don't do this, people will die.' You can all supply your own this: 'If we don't collect this type of information,' or 'If we don't use this technique,' or 'If we don't extend this authority.' It is extraordinarily difficult to be the attorney standing in front of the freight train that is the need for this."

He continued: “‘No’ must be spoken into a storm of crisis, with loud voices all around....It takes far more than a sharp legal mind to say ‘no’ when it matters most. It takes moral character. It takes an ability to see the future. It takes an appreciation of the damage that will flow from an unjustified ‘yes.’ It takes an understanding that, in the long-run, intelligence under law is the only sustainable intelligence in this country.”

These words matter now more than ever. Comey and the FBI are standing in front of a freight train and the engine is the White House. They are in charge of an extraordinary counterintelligence investigation that has reached into the Trump administration, and led this week to the dismissal of the president's national security adviser, Michael Flynn. They and their colleagues at the CIA seek to know the scope and depth of the Kremlin's influence on the 2016 presidential election, a covert operation that Senator John McCain has called "an act of war." They are trying to determine the nature of the contacts between Moscow and the Trump campaign during and after Election Day. Ultimately, they will have to ask what the president knew and when he knew it.

Trump is at war with the FBI and the CIA, tweeting denunciations of the agencies and railing against what he calls criminal leaks of information about the investigation. Complicating matters, the president fired Comey’s immediate superior, the acting attorney general, Sally Yates. She was the one who informed the White House that Flynn’s conversations with Russia’s ambassador – and the fact that Flynn was lying about them to superiors up to and including the vice president – made him susceptible to blackmail. Making matters potentially more fraught, the new attorney general, Jeff Sessions, who was a leading figure in the Trump campaign, has said that he would not recuse himself from overseeing the FBI’s investigation.

All this puts Comey – and the president – in a political and legal contretemps at a moment when the stakes could not be higher. Trump cannot fire the FBI director now. That act would be seen as much more than political malfeasance. It could be construed as an obstruction of justice. Yet Comey cannot proceed freely without the knowledge and, in crucial matters, the approval of the attorney general. The likelihood that they will lock horns is high.

If the attorney general orders the FBI investigation quashed in any way – or Trump tells him to do it – that fact will not stay secret for two years, two weeks, or two days. Perhaps two hours at most. Comey would likely resign in protest, taking the upper echelons of the FBI with him. Remember the Saturday Night Massacre of 1973, when President Nixon fired the Watergate special prosecutor seeking his secret White House tapes, and the attorney general and his deputy quit in defiance? That was the beginning of the end of Nixon. President George W. Bush, in his memoirs, says that conflagration immediately crossed his mind during his 2004 White House confrontation with Comey.

If we go down that road now, the Saturday Night Massacre will look like a Sunday morning prayer breakfast by contrast.

One wonders what Hillary Clinton makes of all this. She pointedly blamed Comey for the outcome of the election. On July 5, he criticized her "extremely careless" handling of classified information in her use of a private e-mail server, handing Trump an issue which he hammered every chance he had. Comey's statement was gratuitous; carelessness is not a violation of federal law. Then, on Oct. 28, with the election 11 days away, Comey sent a letter to Congress – instantly leaked by Republican Hillary hunters in the House of Representatives – saying that there might be more e-mails to examine. (As it turned out, that was a false alarm, but it sent the flames higher.)

"We don't ordinarily tell Congress about ongoing investigations," Comey wrote in an e-mail to his agents after sending the fateful letter to Capitol Hill. But, he added, "it would be misleading to the American people were we not to supplement the record." He felt, according to very senior FBI officials, that he'd be damned if he did and damned if he didn't keep Congress informed. In any case, he was damned.

Comey is now in charge of one of the most delicate, and potentially the most dangerous, counterintelligence cases in the 108-year history of the FBI. Knowing his record, I suspect he would rather run naked down Pennsylvania Avenue than disclose the details of this investigation to the American people at this moment. The fact remains that the FBI has the lead in solving a series of mysteries enveloping the Trump campaign team and its all-stars who now run the executive branch of the U.S. government. But in time Senator John McCain will exercise his investigative powers, and he will probably persuade a handful of Republican senators to join him. In the short run, the most important aspects of this case probably will play out in secret, in lead-lined chambers of the Capitol and heavily secured conference rooms at the FBI.

But if we have learned anything about the modern history of the presidency, from the pretend Camelot of John F. Kennedy to the present crises of Donald Trump, it is this: there are no secrets that time will not reveal.