Comey, at a press conference in June 2014, has tackled terrorism, encryption and Apple since taking over the FBI
Melissa Golden—Redux
By Massimo Calabresi
March 31, 2016

Late last summer, the director of the Federal Bureau of Investigation, James Comey, met with John Giacalone, the bureau official responsible for everything from counterterrorism to counterintelligence across the U.S. Giacalone, a fireplug of a man who started out as a New York City field agent battling organized crime in the 1990s, wanted to brief Comey on a high-profile issue that had been referred to the bureau by the Inspector General of the Intelligence Community. Emails found on the private, unclassified server used by Hillary Clinton as Secretary of State contained classified information; Giacalone’s National Security Branch wanted to investigate how the secrets got there and whether anyone had committed a crime in the process. Comey was clear about one thing. “He wanted to make sure it was treated the same way as all other cases,” says Giacalone, who left the bureau in February.

Seven months later, 20 to 30 agents, technical specialists and analysts have been assigned to the investigation, according to sources familiar with it. The agents have conducted interviews and done forensic analysis of the evidence collected. And they have executed process, the sources say, referring to a category of investigative tools that can include, among other things, subpoenas. As they near the end of the investigation, the agents are preparing to interview several of Clinton’s closest aides, and perhaps the candidate herself, according to the sources, a move Clinton campaign officials say she will comply with. Attorney General Loretta Lynch told Congress on Feb. 24 that she is awaiting a recommendation from Comey and the FBI on whether anyone should be charged.

Many Americans have come to know Comey, 55, as the face of the FBI in its fight with Apple over access to the encrypted iPhone used by one of the ISIS followers who killed 14 people in San Bernardino, Calif., on Dec. 2. After the Justice Department sued Apple for access to the contents of the phone, Comey spoke about the dangers of the company’s resistance and its widespread use of encryption. Apple CEO Tim Cook pushed back hard, saying in an interview with TIME that the FBI’s request “could wind up putting millions of customers at risk.” Then, just a day before a key hearing on March 22, the bureau backed down. A week later, it announced it had gained access to the phone through an unidentified third party and no longer needed Apple’s help. The bureau has since dropped the case, but the episode is a reminder of the deepening complexity of law enforcement in a digital age.

Compared with solving the Apple puzzle, the case of the Clinton emails looks on the surface like a straight-up job, the kind of leak investigation the bureau undertakes several times a year. But these are not straight-up times. Clinton is the front runner for the Democratic nomination. Some 67% of Americans already say she is neither honest nor trustworthy, according to a February poll by Quinnipiac University. That impression is bolstered by the steps she and her aides took that kept even her routine State Department emails beyond the reach of normal federal record-keeping procedures, an effort made clear in emails released in the wake of lawsuits brought under the Freedom of Information Act over the past 18 months. If FBI agents take steps that suggest Clinton is personally under suspicion, it could change the course of the campaign.

Comey is keeping a close watch on the investigation, getting briefings from team leaders and personally overseeing the case. Agents have been told they may be polygraphed to prevent leaks, the sources familiar with the probe say. “I want to ensure [the Clinton email investigation] is done in the ways the FBI does all its work: professionally, with integrity, promptly,” Comey told Congress in February. “And without any interference whatsoever.”

When the agents have run down all their leads, the sources say, Comey will present the evidence to Lynch, along with his assessment of what it shows. Some Republicans are referring to his recommendation as the “Comey primary” in the hopes it will sway the election their way. That may be wishful thinking, but one thing is clear: Comey has spent much of his career investigating and occasionally confronting high-profile public figures.

Every morning at 7:30 when Comey arrives for work at the bureau’s ugly and brooding concrete headquarters on Pennsylvania Avenue, the name over the door serves as a reminder that the FBI has sometimes played by its own rules. The bureau’s first leader, J. Edgar Hoover, for whom the building is named, spied on everyone from Cabinet officials to political dissidents and even tried to blackmail Martin Luther King Jr., whom he viewed as a national-security threat. Mindful of that history, Presidents have more recently chosen FBI directors with a puritanical devotion to political independence. Louis Freeh and Robert Mueller were obsessively upright former prosecutors. Freeh viewed himself as a scourge of politicized justice, real or imagined; Mueller, a former Marine, ruled the FBI with an iron fist as he remade it after 9/11. Both came into conflict with the Presidents who had appointed them.

Comey too comes from the world of federal prosecutors and projects the same air of rectitude that Freeh and Mueller do. Growing up in New Jersey, he had planned on being a doctor, but after taking a course on death at the College of William and Mary, he ended up graduating with a double major in chemistry and religion. He met his wife of 28 years there (they have five children), then went on to law school at the University of Chicago and clerked on the federal appeals court in lower Manhattan. In 1987, Rudy Giuliani hired him as an attorney in the powerful prosecutor’s office of the Southern District of New York.

It was in the 1990s that Comey got his first experience navigating the treacherous confluence of law and politics. Looking to get back into government after a stint in private practice, Comey signed on as deputy special counsel to the Senate Whitewater Committee, impaneled to look into, among other things, a minor Clinton real estate deal gone bad. In 1996, after months of work, Comey came to some damning conclusions: Hillary Clinton was personally involved in mishandling documents and had ordered others to block investigators as they pursued their case. Worse, her behavior fit into a pattern of concealment: she and her husband had tried to hide their roles in two other matters under investigation by law enforcement. Taken together, the interference by White House officials, which included destruction of documents, amounted to “far more than just aggressive lawyering or political naiveté,” Comey and his fellow investigators concluded. It constituted “a highly improper pattern of deliberate misconduct.”

It wasn’t the last time he would cross paths with the Clintons. Comey parlayed the Whitewater job into top posts in Virginia and New York, returning to Manhattan in 2002 to be the top federal prosecutor there. One of his first cases 15 years earlier had been the successful prosecution of Marc Rich, a wealthy international financier. But on his last day as President in 2001, Bill Clinton pardoned Rich. “I was stunned,” Comey later told Congress. As top U.S. prosecutor in New York in 2002, appointed by George W. Bush, Comey inherited the criminal probe into the Rich pardon and 175 others Clinton had made at the 11th hour.

Despite evidence that several pardon recipients, including Rich, had connections to donations to Bill Clinton’s presidential library and Hillary Clinton’s 2000 Senate campaign, Comey found no criminal wrongdoing. He was careful not to let the investigation be used for political purposes by either party. When pressed for details in one case, he said, “I can’t really go into it because it was an investigation that didn’t result in charges. That may be a frustrating answer, but that’s the one I’m compelled to give.”

Comey’s probity didn’t prevent him from taking on other high-profile cases. He once said prosecutors who amassed perfect records at trial by taking only easy, noncontroversial cases were members of the “chickensh-t club,” according to several assistant U.S. Attorneys who worked for him. Comey showed he meant it in 2003, when he led the case against Martha Stewart for making false statements during an insider-trading investigation. He won a conviction on all counts thanks to the testimony of one witness, but it was a close call. Comey later said he had almost not taken the case but chose to risk it because he thought that his hesitation was due to Stewart’s “being rich and famous, and [that] it shouldn’t be that way.”

Clearing Clinton in the pardons case didn’t hurt Comey with Bush. In 2003, Bush promoted him to be Attorney General John Ashcroft’s No. 2. GOP hard-liners would quickly come to rue the pick. Filling in for Ashcroft, who recused himself from the case, Comey appointed his old partner in New York Mob prosecutions, Patrick Fitzgerald, to look into the leak of the identity of CIA officer Valerie Plame, a case that would ultimately snare Vice President Dick Cheney’s chief of staff Scooter Libby and damage the White House in the aftermath of the Iraq War.

Comey’s most dramatic moment came in a 2004 confrontation with Bush’s White House counsel, Alberto Gonzales. The Justice Department had concluded that part of the National Security Agency’s Stellar Wind program of blanket telephone-metadata collection was illegal. Comey, who was running the department after Ashcroft went on leave with a sudden illness, refused to recertify the legality of the program when it expired in March 2004, though West Wing hard-liners led by Cheney were pushing hard for it. Late on the evening of March 10, Comey heard that Gonzales was on his way to George Washington Hospital in Foggy Bottom to try to get the bedridden Ashcroft to sign an authorization for Stellar Wind instead. Comey ordered his FBI driver to speed him to the hospital, lights flashing, in an attempt to prevent it.

Comey arrived minutes before Gonzales, and after pushing his 6-ft. 8-in. frame up several flights of stairs, briefed the semiconscious Ashcroft on what was about to happen. With the help of then FBI Director Mueller, Comey assumed authority over the security detail in the room. Others present worried there might be an armed confrontation between those agents and Gonzales’ Secret Service detail if Gonzales attempted to have Comey removed from the room. But when Gonzales arrived and asked Ashcroft to authorize Stellar Wind, Ashcroft rebuffed him, telling him Comey was in charge. Gonzales left empty-handed.

Days later, after Comey, Mueller and other top Justice Department officials threatened to resign if Bush ordered the NSA to continue using Stellar Wind without the department’s approval, Bush altered the secret program to comply with their legal requirements. Comey “was miraculously great,” says Harvard law professor Jack Goldsmith, who was one of a handful of witnesses to the hospital scene as a top Justice Department lawyer.

Comey’s stand against Gonzales didn’t end there, and its fallout has implications for the current Clinton email case. In May 2007, Comey had left government, and Gonzales, who had replaced Ashcroft atop the Justice Department, was clinging to his job amid unrelated scandals. Comey surprised the top Democratic staffer on the Senate Judiciary Committee by agreeing to make public the details of the hospital-room encounter for the first time in compelling open testimony. The hearing was designed to force Gonzales out, and ultimately it worked. Comey’s testimony led to the discovery by White House lawyers that Gonzales had improperly stored classified notes on Stellar Wind, which in turn led to his resignation that August, according to top Bush White House officials. Comey and Gonzales both declined to comment on the matter.

Comey’s testimony enraged hard-liners but earned him unrivaled respect in Congress and at Justice, where top officials have long understood the challenge of remaining independent of political influence. Comey’s most important supporter turned out to be President Obama’s first Attorney General, Eric Holder. Comey had bluntly criticized Holder for approving the Marc Rich pardon as acting Attorney General on Clinton’s last day in office, calling it a “huge misjudgment.” But Comey told Congress that Holder had paid for the error “dearly in reputation.” When Mueller stepped down in 2013, Holder recommended Comey, a Republican, as one of two candidates to take over the FBI.

In his early days as FBI boss, top aides say, Comey thought terrorism might be a fading problem. Osama bin Laden was dead, al-Qaeda’s core had been severely weakened, and ISIS was little more than a band of fanatics operating in the no-man’s-land between Syria and Iraq. But after the terrorist group’s surge toward Baghdad in the first half of 2014, Obama approved air strikes against it. Within weeks, the group began beheading American captives, and a leading ISIS figure, Abu Muhammad al-Adnani, posted an English-language call to arms for followers to attack Americans around the world. Within months, FBI agents reported a spike in the number of possible ISIS followers in the U.S.

Comey responded with more agents and an increased emphasis on intelligence collection. In 2015, the bureau saw only a slight increase in the overall number of arrests of those supporting terrorists in the U.S. but a fivefold increase in the number of those arrested who followed ISIS. “This ISIL threat is not your parents’ al-Qaeda,” Comey told House members on Feb. 25. He says terrorists no longer hatch plots in faraway places but rather “crowdsource” terrorism by inspiring and motivating domestic supporters like the couple behind the San Bernardino attack.

That event merged with the second big challenge of his tenure: the danger of criminals and terrorists “going dark” as encryption becomes more widely used. Comey says the use of encrypted smartphones means his agents can’t collect evidence to prosecute and prevent crimes and terrorist attacks, even when they have a court warrant. Comey, who uses a government-issued phone for work and has an iPhone for personal use, told the House in February, “These phones are wonderful. I love them.” But he argued two days earlier that there are “increasing situations where we cannot, with lawful court orders, read the communications of terrorists, gangbangers, pedophiles–all different kinds of bad people.”

This concern drove Comey’s highest-profile moment so far in his job atop the FBI. Within hours of the San Bernardino attack, agents recovered the government-issued iPhone 5c of shooter Syed Farook. After getting a court-ordered warrant, the FBI took the phone to its Regional Computer Forensic Laboratory and, with the help of Apple, gained access to information stored in the phone’s server-based account. But when the agents tried to access the phone’s internal records, they couldn’t get past the four-digit pass code, which was set to wipe the phone’s memory after more than 10 failed tries. When Apple refused to create software to circumvent that feature, Comey approved taking the company to court. On March 28 the Justice Department announced it did not need Apple to crack the phone after all.

For now, Comey’s power to access every Apple phone in the world remains hypothetical; the potential effect of the Clinton email probe on the presidential election is very real. The State Department has said that 22 of the documents on Clinton’s private server contained information classified at the highest level, top secret. Those documents were based on intelligence generated not by State but by other agencies like the CIA and NSA. Because those secrets tend to come from some of the government’s most sensitive sources, such as human spies or expensive satellites, they are protected by special penalties under the Espionage Act, which provides for up to 10 years in prison for some violations.

But none of the classified documents found on Clinton’s server was marked classified when it was sent or received. And the standard for conviction in a leak case is high: the suspect must knowingly store the secrets improperly or show gross negligence in their handling. In most cases, Clinton’s close aides received documents from others in the department and passed them along to their boss. To figure out if anyone acted knowingly or with gross negligence, agents have conducted interviews. The Justice Department has reached an immunity agreement with the aide who set up Clinton’s server.

There is always a chance that agents poring over Clinton’s 50,000 pages of emails could come across something unrelated that they think warrants a closer look and the investigation could spread. That is how the probe of a busted land deal in 1994 led to the impeachment of Bill Clinton four years later over lying about an affair. While there have been multiple reports of foreign companies and countries making contributions to Bill Clinton’s foundation or paying him for speeches at the same time that they had issues before the State Department, it is far from clear that any of that would be a violation of law, whatever some Republicans might hope. But the FBI’s Domestic Investigations and Operations Guide sets a very low bar for an initial information-gathering effort known as an “assessment.”

The classification probe remained an assessment for a time but is now an investigation, according to the sources familiar with it. The FBI will be looking not only at the handling of classified information but also at the Clinton team’s response to the probe itself. Clinton erased 30,000 personal emails from her private server before handing it over to investigators. Republicans have repeatedly alleged, without proof, that in the process she destroyed incriminating evidence about her handling of government matters, including the attack by terrorists on the U.S. outpost in Benghazi, Libya.

Lawyers preparing Clinton and her aides for possible interviews are well aware that Comey has a history of prosecuting those who impede investigators. Cheney’s aide Libby was convicted not of leaking Plame’s identity but of obstructing justice, as was Martha Stewart. Comey had a front-row seat to Clinton’s controversial handling of documents in the Whitewater case. Ultimately the Senate committee he worked for two decades ago found no criminal wrongdoing but issued a politically damaging report anyway. Clinton campaign official Brian Fallon says that the FBI has not requested an interview with her yet and that she remains ready to cooperate with the probe. “She first expressed her willingness to cooperate in any way possible last August,” says Fallon, “and that included offering to meet with them and answer any questions they might have.”

Comey’s recommendation to Lynch, when it comes, could include a description of the evidence; what laws, if any, might have been violated; and how confident he is in the results of the probe, the sources familiar with the investigation tell TIME. What will come of the Comey primary? Says Giacalone: “If the evidence is there, it’s there. If it leads to something inconclusive, or nothing, he’s not going to recommend filing charges.”

Contact us at editors@time.com.

This appears in the April 11, 2016 issue of TIME.

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