Primer: This summary places events in a timeline and context. There are some additional details and the text appears to be fair. Further, when Loretta Lynch refers to the investigation as a ‘matter’, it for the most parts tells us all we need to know.

Comey Tried to
Shield the F.B.I. From
Politics. Then He
Shaped an Election.

As the F.B.I. investigated Hillary Clinton and the Trump
campaign, James B. Comey tried to keep the bureau out
of politics but plunged it into the center of a bitter election.

New York Times/WASHINGTON — The day before he upended the 2016 election, James B. Comey, the director of the Federal Bureau of Investigation, summoned agents and lawyers to his conference room. They had been debating all day, and it was time for a decision.

Mr. Comey’s plan was to tell Congress that the F.B.I. had received new evidence and was reopening its investigation into Hillary Clinton, the presidential front-runner. The move would violate the policies of an agency that does not reveal its investigations or do anything that may influence an election. But Mr. Comey had declared the case closed, and he believed he was obligated to tell Congress that had changed.

“Should you consider what you’re about to do may help elect Donald Trump president?” an adviser asked him, Mr. Comey recalled recently at a closed meeting with F.B.I. agents.

He could not let politics affect his decision, he replied. “If we ever start considering who might be affected, and in what way, by what we do, we’re done,” he told the agents.

But with polls showing Mrs. Clinton holding a comfortable lead, Mr. Comey ended up plunging the F.B.I. into the molten center of a bitter election. Fearing the backlash that would come if it were revealed after the election that the F.B.I. had been investigating the next president and had kept it a secret, Mr. Comey sent a letter informing Congress that the case was reopened.

For Mr. Comey, keeping the F.B.I. out of politics is such a preoccupation that he once said he would never play basketball with President Barack Obama because of the appearance of being chummy with the man who appointed him. But in the final months of the presidential campaign, the leader of the nation’s pre-eminent law enforcement agency shaped the contours, if not the outcome, of the presidential race by his handling of the Clinton and Trump-related investigations.

An examination by The New York Times, based on interviews with more than 30 current and former law enforcement, congressional and other government officials, found that while partisanship was not a factor in Mr. Comey’s approach to the two investigations, he handled them in starkly different ways. In the case of Mrs. Clinton, he rewrote the script, partly based on the F.B.I.’s expectation that she would win and fearing the bureau would be accused of helping her. In the case of Mr. Trump, he conducted the investigation by the book, with the F.B.I.’s traditional secrecy. Many of the officials discussed the investigations on the condition of anonymity because they were not authorized to speak to reporters.

Mr. Comey made those decisions with the supreme self-confidence of a former prosecutor who, in a distinguished career, has cultivated a reputation for what supporters see as fierce independence, and detractors view as media-savvy arrogance.

The Times found that this go-it-alone strategy was shaped by his distrust of senior officials at the Justice Department, who he and other F.B.I. officials felt had provided Mrs. Clinton with political cover. The distrust extended to his boss, Loretta E. Lynch, the attorney general, who Mr. Comey believed had subtly helped play down the Clinton investigation.

His misgivings were only fueled by the discovery last year of a document written by a Democratic operative that seemed — at least in the eyes of Mr. Comey and his aides — to raise questions about her independence. In a bizarre example of how tangled the F.B.I. investigations had become, the document had been stolen by Russian hackers.

The examination also showed that at one point, President Obama himself was reluctant to disclose the suspected Russian influence in the election last summer, for fear his administration would be accused of meddling.

Mr. Comey, the highest-profile F.B.I. director since J. Edgar Hoover, has not squarely addressed his decisions last year. He has touched on them only obliquely, asserting that the F.B.I. is blind to partisan considerations. “We’re not considering whose ox will be gored by this action or that action, whose fortune will be helped,” he said at a public event recently. “We just don’t care. We can’t care. We only ask: ‘What are the facts? What is the law?’”

But circumstances and choices landed him in uncharted and perhaps unwanted territory, as he made what he thought were the least damaging choices from even less desirable alternatives.

“This was unique in the history of the F.B.I.,” said Michael B. Steinbach, the former senior national security official at the F.B.I., who worked closely with Mr. Comey, describing the circumstances the agency faced last year while investigating both the Republican and Democratic candidates for president. “People say, ‘This has never been done before.’ Well, there never was a before. Or ‘That’s not normally how you do it.’ There wasn’t anything normal about this.”

‘Federal Bureau of Matters’

The script had been edited and revised several times, former officials said. Mr. Strzok, Mr. Steinbach, lawyers and others debated every phrase. Speaking so openly about a closed case is rare, and the decision to do so was not unanimous, officials said. But the team ultimately agreed that there was an obligation to inform American voters.

Mr. Comey’s criticism — his description of her carelessness — was the most controversial part of the speech. Agents and prosecutors have been reprimanded for injecting their legal conclusions with personal opinions. But those close to Mr. Comey say he has no regrets.

By scolding Mrs. Clinton, Mr. Comey was speaking not only to voters but to his own agents. While they agreed that Mrs. Clinton should not face charges, many viewed her conduct as inexcusable. Mr. Comey’s remarks made clear that the F.B.I. did not approve.

At the Justice Department, frustrated prosecutors said Mr. Comey should have consulted with them first. Mrs. Clinton’s supporters said that Mr. Comey’s condemnations seemed to make an oblique case for charging her, undermining the effect of his decision.

In the days after the announcement, Mr. Comey and Ms. Lynch each testified before Congress, with different results. Neither the F.B.I. nor the Justice Department normally gives Congress a fact-by-fact recounting of its investigations, and Ms. Lynch spent five hours avoiding doing so.

“I know that this is a frustrating exercise for you,” she told the House Judiciary Committee.

Mr. Comey discussed his decision to close the investigation and renewed his criticism of Mrs. Clinton.

And with both parties angry at him, he had proved yet again that he was willing to speak his mind, regardless of the blowback. He seemed to have safely piloted the F.B.I. through the storm of a presidential election.

But as Mr. Comey moved past one tumultuous investigation, another was about to heat up.

Russia Rising

Days after Mr. Comey’s news conference, Carter Page, an American businessman, gave a speech in Moscow criticizing American foreign policy. Such a trip would typically be unremarkable, but Mr. Page had previously been under F.B.I. scrutiny years earlier, as he was believed to have been marked for recruitment by Russian spies. And he was now a foreign policy adviser to Mr. Trump.

“Russia, if you’re listening,” he said, “I hope you’ll be able to find the 30,000 emails that are missing.”

In late July, the F.B.I. opened an investigation into possible collusion between members of Mr. Trump’s campaign and Russian operatives. Besides Mr. Comey and a small team of agents, officials said, only a dozen or so people at the F.B.I. knew about the investigation. Mr. Strzok, just days removed from the Clinton case, was selected to supervise it.

In late August, Mr. Comey and his deputies were briefed on a provocative set of documents about purported dealings between shadowy Russian figures and Mr. Trump’s campaign. One report, filled with references to secret meetings, spoke ominously of Mr. Trump’s “compromising relationship with the Kremlin” and threats of “blackmail.”

Mr. Steele had been a covert agent for MI6 in Moscow, maintained deep ties with Russians and worked with the F.B.I., but his claims were largely unverified. It was increasingly clear at the F.B.I. that Russia was trying to interfere with the election.

As the F.B.I. plunged deeper into that investigation, Mr. Comey became convinced that the American public needed to understand the scope of the foreign interference and be “inoculated” against it.

The president replied that going public would play right into Russia’s hands by sowing doubts about the election’s legitimacy. Mr. Trump was already saying the system was “rigged,” and if the Obama administration accused Russia of interference, Republicans could accuse the White House of stoking national security fears to help Mrs. Clinton.

Mr. Comey argued that he had unique credibility to call out the Russians and avoid that criticism. After all, he said, he had just chastised Mrs. Clinton at his news conference.

But John O. Brennan, the C.I.A. director, was so concerned about the Russian threat that he gave an unusual private briefing in the late summer to Harry Reid, then the Senate Democratic leader.

Mr. Comey knew the investigation of the Trump campaign was just underway, and keeping with policy, he said nothing about it.

Mr. Reid’s letter sparked frenzied speculation about what the F.B.I. was doing. At a congressional hearing in September, Representative Jerrold Nadler, Democrat of New York, pressed Mr. Comey for an explanation, citing his willingness to give details about his investigation of Mrs. Clinton.

But Mr. Comey never considered disclosing the case. Doing so, he believed, would have undermined an active investigation and cast public suspicion on people the F.B.I. could not be sure were implicated.

“I’m not confirming that we’re investigating people associated with Mr. Trump,” Mr. Comey said to Mr. Nadler. “In the matter of the email investigation, it was our judgment — my judgment and the rest of the F.B.I.’s judgment — that those were exceptional circumstances.”

Even in classified briefings with House and Senate intelligence committee members, Mr. Comey repeatedly declined to answer questions about whether there was an investigation of the Trump campaign.

To Mr. Comey’s allies, the two investigations were totally different. One was closed when he spoke about it. The other was continuing, highly classified and in its earliest stages. Much of the debate over Mr. Comey’s actions over the last seven months can be distilled into whether people make that same distinction.

The agent said that if Mr. Steele could get solid corroboration of his reports, the F.B.I. would pay him $50,000 for his efforts, according to two people familiar with the offer. Ultimately, he was not paid.

But by fall, the gravity of the Russian effort to affect the presidential election had become clear.

The D.N.C. hack and others like it had once appeared to be standard Russian tactics to tarnish a Western democracy. After the WikiLeaks disclosures and subsequent leaks by a Russian group using the name DCLeaks, agents and analysts began to realize that Moscow was not just meddling. It was trying to tip the election away from Mrs. Clinton and toward Mr. Trump.

At their second meeting, Mr. Comey argued that it would look too political for the F.B.I. to comment so close to the election, according to several people in attendance. Officials in the room felt whiplashed. Two months earlier, Mr. Comey had been willing to put his name on a newspaper article; now he was refusing to sign on to an official assessment of the intelligence community.

That night, WikiLeaks began posting thousands of hacked emails from another source: the private email account of John D. Podesta, chairman of the Clinton campaign.

The emails included embarrassing messages between campaign staff members and excerpts from Mrs. Clinton’s speeches to Wall Street. The disclosure further convinced the F.B.I. that it had initially misread Russia’s intentions.

“You may be aware that your emails have been hacked,” an agent told him.

Mr. Podesta laughed. The same agency that had so thoroughly investigated Mrs. Clinton, he said, seemed painfully slow at responding to Russian hacking.

“Yes,” he answered. “I’m aware.”

Supplementing the Record

The Daily Mail, a British tabloid, was first with the salacious story: Anthony D. Weiner, the former New York congressman, had exchanged sexually charged messages with a 15-year-old girl.

F.B.I. agents in New York seized Mr. Weiner’s laptop in early October. The investigation was just one of many in the New York office and was not treated with great urgency, officials said. Further slowing the investigation, the F.B.I. software used to catalog the computer files kept crashing.

Eventually, investigators realized that they had hundreds of thousands of emails, many of which belonged to Ms. Abedin and had been backed up to her husband’s computer.

Neither Mr. Comey nor Ms. Lynch was concerned. Agents had discovered devices before in the Clinton investigation (old cellphones, for example) that turned up no new evidence.

Then, agents in New York who were searching image files on Mr. Weiner’s computer discovered a State Department document containing the initials H.R.C. — Hillary Rodham Clinton. They found messages linked to Mrs. Clinton’s home server.

And they made another surprising discovery: evidence that some of the emails had moved through Mrs. Clinton’s old BlackBerry server, the one she used before moving to her home server. If Mrs. Clinton had intended to conceal something, agents had always believed, the evidence might be in those emails. But reading them would require another search warrant, essentially reopening the Clinton investigation.

The election was two weeks away.

Mr. Comey learned of the Clinton emails on the evening of Oct. 26 and gathered his team the next morning to discuss the development.

Seeking a new warrant was an easy decision. He had a thornier issue on his mind.

Back in July, he told Congress that the Clinton investigation was closed. What was his obligation, he asked, to acknowledge that this was no longer true?

It was a perilous idea. It would push the F.B.I. back into the political arena, weeks after refusing to confirm the active investigation of the Trump campaign and declining to accuse Russia of hacking.

The question consumed hours of conference calls and meetings. Agents felt they had two options: Tell Congress about the search, which everyone acknowledged would create a political furor, or keep it quiet, which followed policy and tradition but carried its own risk, especially if the F.B.I. found new evidence in the emails.

“In my mind at the time, Clinton is likely to win,” Mr. Steinbach said. “It’s pretty apparent. So what happens after the election, in November or December? How do we say to the American public: ‘Hey, we found some things that might be problematic. But we didn’t tell you about it before you voted’? The damage to our organization would have been irreparable.”

Conservative news outlets had already branded Mr. Comey a Clinton toady. That same week, the cover of National Review featured a story on “James Comey’s Dereliction,” and a cartoon of a hapless Mr. Comey shrugging as Mrs. Clinton smashed her laptop with a sledgehammer.

Congressional Republicans were preparing for years of hearings during a Clinton presidency. If Mr. Comey became the subject of those hearings, F.B.I. officials feared, it would hobble the agency and harm its reputation. “I don’t think the organization would have survived that,” Mr. Steinbach said.

The assumption was that the email review would take many weeks or months. “If we thought we could be done in a week,” Mr. Steinbach said, “we wouldn’t say anything.”

The spirited debate continued when Mr. Comey reassembled his team later that day. F.B.I. lawyers raised concerns, former officials said. But in the end, Mr. Comey said he felt obligated to tell Congress.

“I went back and forth, changing my mind several times,” Mr. Steinbach recalled. “Ultimately, it was the right call.”

That afternoon, Mr. Comey’s chief of staff called the office of Ms. Yates, the deputy attorney general, and revealed the plan.

When Ms. Lynch was told, she was both stunned and confused. While the Justice Department’s rules on “election year sensitivities” do not expressly forbid making comments close to an election, administrations of both parties have interpreted them as a broad prohibition against anything that may influence a political outcome.

Ms. Lynch understood Mr. Comey’s predicament, but not his hurry. In a series of phone calls, her aides told Mr. Comey’s deputies that there was no need to tell Congress anything until agents knew what the emails contained.

Either Ms. Lynch or Ms. Yates could have ordered Mr. Comey not to send the letter, but their aides argued against it. If Ms. Lynch issued the order and Mr. Comey obeyed, she risked the same fate that Mr. Comey feared: accusations of political interference and favoritism by a Democratic attorney general.

If Mr. Comey disregarded her order and sent the letter — a real possibility, her aides thought — it would be an act of insubordination that would force her to consider firing him, aggravating the situation.

So the debate ended at the staff level, with the Justice Department imploring the F.B.I. to follow protocol and stay out of the campaign’s final days. Ms. Lynch never called Mr. Comey herself.

The next morning, Friday, Oct. 28, Mr. Comey wrote to Congress, “In connection with an unrelated case, the F.B.I. has learned of the existence of emails that appear to be pertinent to the investigation.”

His letter became public within minutes. Representative Jason Chaffetz of Utah, a Republican and a leading antagonist of Mrs. Clinton’s, jubilantly announced on Twitter, “Case reopened.”

‘This Changes Everything’

The Clinton team was outraged. Even at the F.B.I., agents who supported their high-profile director were stunned. They knew the letter would call into question the F.B.I.’s political independence.

Mr. Trump immediately mentioned it on the campaign trail. “As you might have heard,” Mr. Trump told supporters in Maine, “earlier today, the F.B.I. … ” The crowd interrupted with a roar. Everyone had heard.

Polls almost immediately showed Mrs. Clinton’s support declining. Presidential races nearly always tighten in the final days, but some political scientists reported a measurable “Comey effect.”

“This changes everything,” Mr. Trump said.

Mr. Comey explained in an email to his agents that Congress needed to be notified. “It would be misleading to the American people were we not to supplement the record,” he wrote.

But many agents were not satisfied.

At the Justice Department, career prosecutors and political appointees privately criticized not only Mr. Comey for sending the letter but also Ms. Lynch and Ms. Yates for not stopping him. Many saw the letter as the logical result of years of not reining him in.

Mr. Comey told Congress that he had no idea how long the email review would take, but Ms. Lynch promised every resource needed to complete it before Election Day.

At the F.B.I., the Clinton investigative team was reassembled, and the Justice Department obtained a warrant to read emails to or from Mrs. Clinton during her time at the State Department. As it turned out, only about 50,000 emails met those criteria, far fewer than anticipated, officials said, and the F.B.I. had already seen many of them.

Mr. Comey was again under fire. Former Justice Department officials from both parties wrote a Washington Post op-ed piece titled “James Comey Is Damaging Our Democracy.”

At a Justice Department memorial for Mr. Margolis, organizers removed all the chairs from the stage, avoiding the awkward scene of Mr. Comey sitting beside some of his sharpest critics.

Jamie S. Gorelick, a deputy attorney general during the Clinton administration, eulogized Mr. Margolis for unfailingly following the rules, even when facing unpopular options. Audience members heard it as a veiled critique of both Mr. Comey and Ms. Lynch.

On Nov. 5, three days before Election Day, Mr. Strzok and his team had 3,000 emails left to review. That night, they ordered pizza and dug in. At about 2 a.m., Mr. Strzok wrote an email to Mr. Comey and scheduled it to send at 6 a.m. They were finished.

A few hours later, Mr. Strzok and his team were back in Mr. Comey’s conference room for a final briefing: Only about 3,000 emails had been potentially work-related. A dozen or so email chains contained classified information, but the F.B.I. had already seen it.

And agents had found no emails from the BlackBerry server during the crucial period when Mrs. Clinton was at the State Department.

Nothing had changed what Mr. Comey had said in July.

That conclusion was met with a mixture of relief and angst. Everyone at the meeting knew that the question would quickly turn to whether Mr. Comey’s letter had been necessary.

That afternoon, Mr. Comey sent a second letter to Congress. “Based on our review,” he wrote, “we have not changed our conclusions.”

Political Consequences

Mr. Comey did not vote on Election Day, records show, the first time he skipped a national election, according to friends. But the director of the F.B.I. was a central story line on every television station as Mr. Trump swept to an upset victory.

Many factors explained Mr. Trump’s success, but Mrs. Clinton blamed just one. “Our analysis is that Comey’s letter — raising doubts that were groundless, baseless, proven to be — stopped our momentum,” she told donors a few days after the election. She pointed to polling data showing that late-deciding voters chose Mr. Trump in unusually large numbers.

Even many Democrats believe that this analysis ignores other factors, but at the F.B.I., the accusation stung. Agents are used to criticism and second-guessing. Rarely has the agency been accused of political favoritism or, worse, tipping an election.

For all the attention on Mrs. Clinton’s emails, history is likely to see Russian influence as the more significant story of the 2016 election. Questions about Russian meddling and possible collusion have marred Mr. Trump’s first 100 days in the White House, cost him his national security adviser and triggered two congressional investigations. Despite Mr. Trump’s assertions that “Russia is fake news,” the White House has been unable to escape its shadow.

Mr. Comey has told friends that he has no regrets, about either the July news conference or the October letter or his handling of the Russia investigation. Confidants like Mr. Richman say he was constrained by circumstance while “navigating waters in which every move has political consequences.”

But officials and others close to him also acknowledge that Mr. Comey has been changed by the tumultuous year.

Early on Saturday, March 4, the president accused Mr. Obama on Twitter of illegally wiretapping Trump Tower in Manhattan. Mr. Comey believed the government should forcefully denounce that claim. But this time he took a different approach. He asked the Justice Department to correct the record. When officials there refused, Mr. Comey followed orders and said nothing publicly.

“Comey should say this on the record,” said Tommy Vietor, a National Security Council spokesman in the Obama administration. “He’s already shattered all norms about commenting on ongoing investigations.”

Mr. Richman sees no conflict, but rather “a consistent pattern of someone trying to act with independence and integrity, but within established channels.”

“His approach to the Russia investigation fits this pattern,” he added.

But perhaps the most telling sign that Mr. Comey may have had enough of being Washington’s Lone Ranger occurred last month before the House Intelligence Committee.

Early in the hearing, Mr. Comey acknowledged for the first time what had been widely reported: The F.B.I. was investigating members of the Trump campaign for possible collusion with Russia.

Yet the independent-minded F.B.I. director struck a collaborative tone. “I have been authorized by the Department of Justice to confirm,” he began, ushering in the next phase of his extraordinary moment in national politics.

Mr. Comey was still in the spotlight, but no longer alone.