As the United States attorney for the Southern District of New York, James B. Comey gave a speech to every new prosecutor he hired. Founded in 1789, the Southern District is the most prestigious post in the Justice Department outside Washington. Wall Street titans and crooked politicians go down to the federal courthouse in lower Manhattan, they go on trial, and they go to prison.

The power of a prosecutor is awesome, as Comey well knew. (There's a reason that the statue of Justice holds a sword along with a scale.) He told the young hotshot lawyers who were joining his team that when they stood up in court and proclaimed, "'I represent the United States of America,' people believe the next thing you say." He said this trust flowed from a reservoir filled by their predecessors over the ages. It imposed on them a duty to use their power with wisdom—to "do the right thing" in the name of the law and the Constitution.

When Comey took command of the Southern District in early 2002, Ground Zero was a war zone ten blocks away. For two years he served as a point man in George W. Bush's counterterrorism campaign, and in late 2003 the president appointed him deputy attorney general of the United States. Comey recited the essence of the speech he gave his new prosecutors at his Senate confirmation hearings. Three months later, the strength of his principles was tested severely. In an epic confrontation over the National Security Agency's program of warrantless wiretapping, Comey stared down the president inside the White House. He said no to his commander in chief.

Comey's reputation for integrity and independence led Barack Obama to make him the seventh FBI director in the nation's history. He was sworn in on September 4, 2013. Three years later, the man known as the straightest of straight shooters shot himself in the foot. The ricocheting bullet scarred his reputation, wounded the American body politic, and lodged in the heart of Hillary Clinton's presidential campaign.

On July 5, 2016, Comey sent an email from the J. Edgar Hoover Building in Washington to every FBI agent in the world. "I am about to walk downstairs to deliver a statement to the media about our investigation of Secretary Clinton's use of a personal email server during her time as Secretary of State," he said. He was going to "provide more detail about our process" than was usual, and he was doing so to satisfy the public's interest. "The confidence of the American people in the FBI is a precious thing," Comey said. "Folks outside the FBI may disagree about the result, but I don't want there to be any doubt that this was done in an apolitical and professional way and that our conclusion is honestly held, carefully considered, and ours alone."

Comey told the press that Clinton's handling of classified information was no crime. She had been "extremely careless," he said, but "no reasonable prosecutor" could bring a case against her.

The decision to close the case did not sit well with Republicans in Congress, who summoned Comey to Capitol Hill for several hearings. On September 7, he wrote his agents again and said that "the case itself was not a cliff-hanger." The hard part had been deciding that "the best way to protect the FBI, the Department of Justice, and the American people's sense of justice was to announce it the way we did—with extraordinary transparency." He decried the idea that the Bureau was being "political."

Clinton had been "extremely careless," he said, but "no reasonable prosecutor" could bring a case against her.

But on October 28, eleven days before the election, Comey lifted the lid off a box of dynamite. He sent a letter to the Hillary hunters in Congress explaining that a separate probe had uncovered a new batch of emails that might be relevant to the closed Clinton case. "We don't ordinarily tell Congress about ongoing investigations," Comey told his agents in an email later that day. Nevertheless, he said, "I feel an obligation to do so given that I testified repeatedly in recent months that our investigation was completed. I also think it would be misleading to the American people were we not to supplement the record."

The consequences were immediate and, for Clinton, devastating. Her poll numbers fell. Donald Trump, who had been pushing the "Crooked Hillary" trope for months, proclaimed that his opponent was on the verge of indictment. The warning was mindlessly repeated by an army of Twitter bots, a prominent Fox News personality, and even Rudy Giuliani, who had, like Comey, once been the U.S. attorney for the Southern District of New York.

The letter had nothing to back it up: There was no new evidence against Clinton. At the time Comey sent it, the FBI didn't even have a warrant to open the new cache of emails. He recognized immediately that the letter was open to misinterpretation, but it didn't matter. Nor did it matter when, about thirty-six hours before the election, he sent a letter reconfirming what he'd said in July: There was no crime, no reason to continue the investigation. In the post-fact world, everyone looked up for a second and then went back to their tweeting.

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Donald Trump won the presidency by about a hundred thousand votes spread across three states. According to Trump's own pollster, just five counties in Florida and Michigan could have flipped the Electoral College. Hillary Clinton is not the only person who thinks Comey tipped the balance. In the black lagoon of Washington politicos, there is something close to a consensus that she might be right. Even Corey Lewandowski, who shilled for Trump on CNN after being fired as his campaign manager, said that the FBI director's "amazing" intervention was a pivotal event.

Comey and his wife had six children; one died nine days after birth. He has taught Sunday school, and in college he wrote a senior thesis about Jerry Falwell and Reinhold Niebuhr's shared belief that Christians have a moral duty to participate in public life. Most people who know him see him as a stand-up guy who has spent his career trying to live up to that ideal, as well as to the obligation he impressed upon his new hires in the Southern District: to do the right thing always, no matter the cost. He knew that the FBI director has a special responsibility to keep himself above politics, to work in the interests of no party but his office, his institution, and his country.

Recently I spoke to Comey's predecessor, Robert S. Mueller III. He declined to discuss Comey, but he did say unequivocally that an FBI director must be nonpartisan. Without question, Comey's prior conduct in office held to this principle in times of great danger.

And yet Comey opened up the hood of American politics and tinkered with the engine on the eve of a most consequential election. "He made a terrible, terrible mistake," a senior member of the Washington establishment told me. "He assumed a prosecutorial function. He didn't have to do it, and he shouldn't have."

"He made a terrible, terrible mistake," a senior member of the Washington establishment told me. "He assumed a prosecutorial function. He didn't have to do it, and he shouldn't have."

Clearly Comey's remark about Clinton being "extremely careless" was a blunder—carelessness is a sin of omission, not a federal crime—but the awful truth is that he thought he had no choice, or at least no good choice. When he sent the October 28 letter, Comey broke a long-standing Justice Department rule against meddling in presidential politics on the eve of an election. But if, as seems likely, Comey believed with everyone else that Clinton was on track to become the next commander in chief, he may have felt compelled by a custom of equally potent provenance. For decades the FBI has checked and confronted the power of the president. This tradition runs from our own time of political torment back through Bill Clinton's presidency all the way to the days of J. Edgar Hoover.

When an FBI director damages a reputation, it's usually someone else's. Comey makes sure that every rookie agent knows the shameful story of Hoover's remorseless attempts to destroy Dr. Martin Luther King Jr. Hoover ran the FBI for forty-eight years, starting in 1924. He began saying no to presidents at the dawn of the cold war, when he openly broke with Harry Truman, testifying before the House Committee on Un-American Activities that the government was soft on communism. Hoover was also contemptuous of John F. Kennedy and his brother Bobby, the attorney general, whose youth and arrogance he despised. In the end he even defied Richard Nixon.

Their clash took place in 1970, after Nixon approved a plan to lift almost every legal restriction on intelligence gathering within the United States. The plan gave the FBI, the CIA, and the NSA the power to eavesdrop on Americans' phone calls, to intercept their mail, and to break into their homes and offices without a warrant. Nixon believed that the only way to stop "revolutionary terrorism" committed by "those who are determined to destroy our society" was to spy on Americans deemed enemies of the state.

Hoover, ever on the watch for what he called "Red fascism," saw the same threat. But he also recognized that the balance between security and liberty, a permanent tension in our democracy, was beginning to tilt toward liberty at the Supreme Court. When Hoover learned that Nixon had only verbally approved the plan and would not sign his name to it, he "went through the ceiling," as his deputy later recalled. Hoover insisted that he was "not going to accept the responsibility myself anymore, even though I've done it for many years."

Hoover's standoff with Nixon wasn't about defending the Constitution. He was afraid he'd be left holding the bag—a black bag containing bugging equipment and burglars' tools. The falling-out over Nixon's warrantless wiretapping plan proved fatal to the longtime alliance between the two men and led directly to political disaster. It also laid the template for four decades of confrontation between the White House and the FBI.

After Hoover said no to Nixon, scuttling his plan to spy on Americans, the president instructed his closest White House aides to create a secret group of wiretappers and burglars—the Plumbers. They conducted espionage and sabotage against Nixon's opponents. The campaign lasted nine months, until the night of June 17, 1972, when the Plumbers were arrested during a black-bag job at the Watergate hotel, where the Democratic party had its headquarters.

The next morning, FBI headquarters was under the watch of Dan Bledsoe, a supervisory special agent in charge of the major-crimes desk. Hoover was six weeks in the grave, and the man running the Bureau day-to-day was Mark Felt—better known as Deep Throat.

Bledsoe told his story for an FBI oral-history project years later: He flipped through the overnight report on the Watergate break-in and saw that the burglars had been in possession of eavesdropping equipment. He immediately opened a criminal case file under the federal wiretapping statutes.

At four in the afternoon, Bledsoe took a call from the White House. He picked up the phone and said, "This is Agent Supervisor Dan Bledsoe. Who am I speaking with?"

"You are speaking with John Ehrlichman. Do you know who I am?" Ehrlichman was the president's right-hand man and had been Hoover's liaison to the Nixon White House. "I have a mandate from the president of the United States," he said. "The FBI is to terminate the investigation of the break-in."

Bledsoe went silent.

"Did you hear what I said?" Ehrlichman thundered. "Are you going to terminate the investigation?"

"No," Bledsoe replied. "Under the Constitution, the FBI is obligated to initiate an investigation to determine whether there has been a violation of the illegal-interception-of-communications statute."

"Do you realize that you are saying no to the president of the United States?"

"Yes."

"Bledsoe, your career is doomed."

The FBI investigation initiated that day led to the political destruction of Richard Nixon and just about everyone else who obstructed justice in his name.

The modern era of the FBI's antagonism toward the White House began on January 19, 1993, in the final hours of George H. W. Bush's presidency. The day before Bill Clinton was sworn into office, the Bureau's director, William Sessions, was hit by a Justice Department report that accused him of petty corruption, including using nearly $10,000 of government money to build a fence at his house. Bush 41 left Sessions as a malevolent parting gift to his successor.

"I have a mandate from the president of the United States," Ehrlichman said. "The FBI is to terminate the investigation of the break-in."

Janet Reno, Clinton's new attorney general, found the FBI in deep disarray. "Quickly, when I came into office, I learned that the FBI didn't know what it had," she later testified. "The right hand didn't know what the left hand was doing." Agents at the dawn of the Internet age lived in a sixty-four-kilobyte world: The Bureau could not put its case files into computers, and agents had no way to connect with one another. On elite terrorist task forces, paper files stacked up on floors and patterns went unseen.

Bill Clinton had many political talents, but the command and control of the Bureau was not among them. The FBI's disastrous 1993 confrontation with the Branch Davidians in Waco, Texas, left some eighty members of the millenarian Christian sect dead, including twenty-five children. It also gave Reno the will to tell the president to dismiss Sessions for his "serious deficiency in judgment." Clinton finally fired him.

The president, to his eternal regret, chose Louis J. Freeh as the new director. A former FBI agent who had joined the Bureau in 1975, a year after Nixon's resignation, Freeh had been a prosecutor and a federal judge in the Southern District of New York. But as Clinton would soon learn, Freeh did not see the president as his boss's boss; he viewed him as a subject of criminal investigations. After Freeh was sworn in, on September 1, 1993, he turned in his White House pass. He spoke with Clinton no more than six times over the seven-plus years he spent in office. John Podesta, Bill Clinton's longtime aide—and Hillary Clinton's 2016 campaign manager—said that the president always referred to his FBI director as "fucking Freeh." Freeh himself wrote in a memoir that Clinton "came to believe that I was trying to undo his presidency." But a president under investigation by the FBI could not, as a matter of politics, fire its director.

Freeh's assault on Clinton started with Whitewater, a labyrinth of innuendo suggesting that Bill and Hillary had been bought off by crooks and swindlers in shady dealings that went back to the beginning of Bill's career in Arkansas. The investigation went on until the end of Clinton's presidency, spawned a special committee in the Senate, and led to the appointment of an independent counsel in 1994. While Whitewater resulted in convictions against several power brokers with roots in Little Rock, it never directly implicated the Clintons in political corruption. Bill Clinton said that the whole investigation was a sham.

But by the time Clinton was sworn in for his second term, in 1997, the president and the FBI were in open war. Freeh and his agents had been investigating the Clintons to no avail, probing for something, anything, to prosecute. Four years and more than $30 million produced nothing of significance until a twenty-four-year-old former White House intern named Monica Lewinsky was interrogated by the FBI.

While Whitewater resulted in convictions against several power brokers with roots in Little Rock, it never directly implicated the Clintons in political corruption.

What followed had to be lived through to be believed. The FBI actually drew blood from a sitting president, executing a court order to extract a DNA sample from Clinton's veins. When it matched the DNA in a telltale semen stain on Lewinsky's famous blue dress, Republicans had the proof they needed that Clinton had lied under oath about sex. The House proceeded to impeachment. A hung verdict in the Senate saved Clinton's presidency. In later years, Lew Merletti, the director of the Secret Service, noted that while the FBI was spending thousands of hours "investigating the foibles of the president and Monica, a number of senior Al Qaeda operatives were traveling the United States."

Whitewater first brought James Comey into public conflict with Hillary Clinton. He joined the Senate Whitewater Committee as a deputy special counsel. The committee dug dry holes regarding Hillary, but Comey and his colleagues had harsh words for her in 1996. They said that she had mishandled sensitive documents and concluded that while her behavior constituted misconduct, no charges against her could be proved. That was two decades ago. Sound familiar?

Comey's time on the Whitewater Committee coincided with the start of the case that made his name as a prosecutor. On June 25, 1996, nineteen American military personnel were killed—372 were wounded—when a tanker truck packed with explosives destroyed the eight-story Khobar Towers housing complex in Dhahran, Saudi Arabia. The dead were members of the U. S. Air Force's 4404th Wing (Provisional), which enforced the no-fly zone over Iraq that was set up after the first Gulf War.

Freeh was justly obsessed with the case, but the FBI's investigation dragged on for five years without resolution. He later spoke about FBI agents sifting through tons of debris in the blazing heat, "sick and dehydrated, working until they literally dropped," digging with their fingers in the desert to find flesh and bone.

The evidence pointed in two directions: homegrown Saudi terrorists and the government of Iran. Freeh tried to persuade Saudi princes to hand over suspects in the case. When his charm offensive failed, he lashed out—first at the royal family, then at the Clinton administration, which he accused of mishandling the case. After federal prosecutors in Washington could not bring the indictment Freeh sought, he concluded that "Khobar represented a national-security threat far beyond the capability or authority of the FBI." By the time George W. Bush was inaugurated in 2001 and the five-year deadline for filing charges drew near, Freeh was preparing to resign.

Comey's time on the Whitewater Committee coincided with the start of the case that made his name as a prosecutor.

Then the Khobar case was handed over to James Comey, who was, at the time, a forty-year-old federal prosecutor in Virginia. On June 21, 2001, four days before the deadline, he brought indictments against Saudi and Lebanese suspects.

That earned Comey his job leading the Southern District of New York. It was a homecoming. Comey had grown up in Yonkers, just outside the city, where his grandfather had worked his way up from street cop to commissioner. As the chief federal prosecutor in Manhattan, Comey would work closely with the head of the FBI: Robert Mueller, a decorated Marine veteran of aristocratic mien.

Mueller had been sworn in on September 4, 2001. A week after claiming his new office, he was thrown into the biggest investigation in the history of the United States. Within twenty-four hours of the airplanes hitting the World Trade Center and the Pentagon, more than half of Mueller's 11,500 FBI agents suddenly found themselves on the terrorism beat. Though the FBI committed some serious abuses against innocent suspects in the days after 9/11, Mueller did not want future historians to write that Americans had won the war on terror but lost their freedom. And yet every day and every hour, the fear of another Al Qaeda attack consumed the Bush White House. The tension between national security and civil liberties ultimately became unbearable.

Comey took another leap up the chain of command after just two years in New York. In December 2003, after reciting his "do the right thing" speech before the Senate Judiciary Committee, he became the number-two man in the Justice Department—and thus Mueller's superior.

Three months after Comey came to Washington as deputy attorney general, he and Mueller went head-to-head with the White House over the National Security Agency's super-secret data-mining programs, collectively code-named Stellar Wind.

Stellar Wind allowed the NSA to eavesdrop on nearly anyone in the United States by assaying the metadata from millions of telephone conversations and emails. It produced an immense torrent of leads—names, telephone numbers, and email addresses—that the NSA passed along to the FBI. Michael Hayden, the NSA chief at the time, said later that the program "turned on the spigot of NSA reporting to FBI in, frankly, an unprecedented way." The Bureau found that digesting all that raw data was like trying to drink from a fire hose.

Within twenty-four hours of the airplanes hitting the World Trade Center and the Pentagon, more than half of Mueller's 11,500 FBI agents suddenly found themselves on the terrorism beat.

The number of people who knew about Stellar Wind was vanishingly small at the start, but by early 2004 it was growing. Comey was read into the program's secret protocols. He became convinced that Stellar Wind was unworkable—and, worse, unconstitutional. (As the Supreme Court would later rule in a pivotal case, a state of war does not make a president king.) In turn, Comey converted Mueller. They agreed that the FBI could not continue to go along with the program. The scope of the searches had to be constrained to protect Americans' rights.

Bush disagreed, of course. So did his White House lawyers. The NSA was a military agency, and therefore, they said, Congress's authorization of military force gave the president the right to electronically eavesdrop on anyone, anywhere in America—free from the constraints of the Fourth Amendment's protections against warrantless searches and seizures.

Comey and Mueller were caught between the president's command and the law of the land. Neither man had seen evidence that the surveillance program had saved a life, stopped an imminent attack, or unveiled an Al Qaeda member in the United States. They also thought it foolhardy that Bush was flouting the Foreign Intelligence Surveillance Court, which had been created after Watergate to oversee national-security wiretapping. The court had been led by an irascible Texan named Royce Lamberth, whose trust Mueller had worked hard to win. FISA judges had approved hundreds of surveillances on the director's word, but Mueller knew that the arrangement was precarious. Lamberth had once destroyed the career of a senior FBI counterintelligence agent who had deceived him. ("We sent a message to the FBI: You've got to tell the truth," the judge said later.)

Stellar Wind had to be reauthorized by the signatures of Bush and John Ashcroft, the attorney general, every forty-five days. Together they had acted on the basis of scary memos from the CIA warning of incessant incoming existential threats. But on March 4, 2004, Comey made the case to Ashcroft that he should not reauthorize Stellar Wind. He was persuasive. That night, the attorney general was felled by a potentially fatal case of gallstone pancreatitis. When Ashcroft was sedated for emergency surgery, Comey became the acting attorney general of the United States.

On the evening of March 10, the day before the next authorization of Stellar Wind was due, Bush ordered his chief of staff, Andy Card, and the White House counsel, Alberto Gonzales, to go to the intensive-care unit at George Washington University Hospital so Ashcroft could sign the reauthorization.

But Ashcroft had come out of surgery the day before and was in no condition to sign secret presidential orders. When Bush called the hospital, at 6:45 in the evening, Ashcroft's wife intercepted the call. The president said it was a matter of national security. She refused to hand over the phone.

The FBI agents who were guarding Ashcroft's room alerted Comey and Mueller that a showdown was imminent. The two men raced to the intensive-care unit in their black cars, sirens blaring. Comey, who is six foot eight, leaped up the stairs two steps at a time and got there first. Ashcroft was fading in and fading out. "I immediately began speaking to him," Comey later testified, "to see if he could focus on what was happening. And it wasn't clear to me that he could. He seemed pretty bad off."

Mueller ordered the FBI agents to make sure that the president's men did not throw Comey out of the hospital room when they arrived. Card and Gonzales entered at 7:35. Gonzales stood at the head of the bed holding a manila envelope with the presidential authorization inside. He told Ashcroft he wanted his signature. Ashcroft lifted his head off his pillow and said no. He did it "in very strong terms," Comey later testified, in an argument "rich in both substance and fact—which stunned me." Then Ashcroft laid down his head and said: "I'm not the attorney general. There is the attorney general." He pointed at Comey.

The president signed the authorization in the White House on the morning of March 11. The next day, Comey and Mueller confronted him. They had resolved to resign in protest, and they planned to take Ashcroft with them.

When Bush realized that his Justice Department and FBI director were rebelling, he recalled the Saturday Night Massacre—the resignations of Elliot Richardson and William Ruckelshaus, Richard Nixon's attorney general and deputy attorney general, on a single day in October 1973, after they each refused the president's order to fire the Watergate special prosecutor. Bush foresaw a political calamity. The headlines would read FBI director and Attorney General resign in protest: can't say why. "I had to make a big decision, and fast," he wrote in his memoir. His reelection was coming up. Bush promised Comey and Mueller in secret that he would step back from the dark side and put Stellar Wind on a legal footing.

That would take years. Comey resigned in 2005, a few months before The New York Times revealed the secret programs. Before he left the Justice Department to become general counsel of Lockheed Martin, the nation's largest military contractor, he told a select audience at the National Security Agency the sort of thing he and Mueller had heard in the White House: "If we don't do this, people will die." Comey told his audience that "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."

Upon this rock Comey's reputation stands—or it did until this past July.

In November, I put a question to Comey through the FBI's chain of command: Why did he feel obliged to tell Congress about the cache of unopened emails at the end of October, before his agents had a warrant to look at them? Comey declined to respond directly, but an FBI official familiar with his thinking explained the gist of the dilemma: The director stood at the fork of two bad roads. Route one: Comey sends the letter to Capitol Hill. A congressman hell-bent on harming Hillary Clinton leaks it. The evidence reveals no crime. Clinton is defeated. Route two: Comey doesn't send the letter. The existence of the emails leaks. Comey is doomed. Another official who works closely with the director put the conundrum in a pithy phrase: "Jim Comey thinks he was handed a shit sandwich."

I also called Ali Soufan, the former FBI supervisory special agent who blew the whistle on the Bush administration's practice of torturing suspected terrorists in secret prisons. He's a highly regarded security-intelligence consultant, and he stays posted on what happens at the highest echelons of the FBI. Soufan told me that he believes Comey was right to go to Congress with what he'd learned. "He had to tell them what happened. But I don't think he paid a lot of attention as to how his statement would be interpreted politically."

Soufan said that the reaction to Comey's letter did "collateral damage" to the Bureau. "All these stories that there was a revolt in the FBI over the Clinton investigation, agents threatening to resign, that Comey was facing a mutiny for failing to recommend charges against Clinton and trying to sway the election for Trump—all false. The cynicism was breathtaking. People did not care about the truth. The entirely fictitious story of an impending indictment on Fox News did political damage. It didn't matter whether it was true or not." The lesson, Soufan said, was that "the FBI needs to be more politically savvy in order to be more apolitical. Comey cannot work as if Washington is the Washington of old. This is not the twentieth century anymore."

Another official who works closely with the director put the conundrum in a pithy phrase: "Jim Comey thinks he was handed a shit sandwich."

Soufan said Comey is "a great guy who operates under the principle that everyone is as principled as him. He is an honorable man operating in a country in which politicians don't operate honorably." He concluded that some of Comey's harshest critics should take stock of the situation in which they, and the country, find themselves: "All these people attacking him don't know how much they are going to need him in the next few years."

Soon after Comey took power at the FBI in September 2013, he stood before President Obama and said that he was under two oaths: "First, the FBI must be independent of all political forces or interests in this country. In a real sense, it must stand apart from other institutions in American life. But second, at the same time, it must be part of the United States Department of Justice, and constrained by the rule of law and the checks and balances built into our brilliant design by our nation's founders." Comey is caught between those conflicting oaths and obligations, at once standing apart from and being a part of a government whose new leaders may besmirch the design of its creators.

For the next seven years, if he serves through the end of his statutory term, Comey will rise before dawn, read through overnight reports about threats to the United States, ride a black car to the White House, and brief the president, if the president will listen. He will report to congressional committees on life-and-death issues of national security. The FBI is fighting battles across the nation and the world, surrounded by real and imagined enemies everywhere you look, and in places you can't see. There are terrorists and cyberwarriors. There are crooks and thieves. There are two houses of Congress. And then there's the White House. Our new president has a history of bending the law nearly to the breaking point. Trump might not like the cut of Jim Comey's jib. But the FBI director must stand up and say no to a president when the Constitution requires it. It's the law, and it's a tradition. We could do worse than having Comey in charge.