Two days before the Inauguration of Donald Trump as the forty-fifth President of the United States, Michael Flynn, a retired lieutenant general and former intelligence officer, sat down in a Washington restaurant. On the tablecloth, he placed a leather-bound folder and two phones, which flashed with text messages and incoming calls. A gaunt, stern-looking man with hooded eyes and a Roman nose, Flynn is sharp in both manner and language. He had been one of Trump’s earliest supporters, a vociferous booster on television, on Twitter, and, most memorably, from the stage of the Republican National Convention. Strident views and a penchant for conspiracy theories often embroiled him in controversy—in a hacked e-mail from last summer, former Secretary of State Colin Powell called him “right-wing nutty”—but Trump rewarded Flynn’s loyalty by making him his national-security adviser. Now, after months of unrelenting scrutiny, Flynn seemed to believe that he could find a measure of obscurity in the West Wing, steps away from Trump and the Oval Office. “I want to go back to having an out-of-sight role,” he told me.

That ambition proved illusory. Three weeks into his job, the Washington Post revealed that Flynn, while he was still a private citizen and Barack Obama was still President, had discussed American sanctions against Russia with Sergey Kislyak, the Russian Ambassador in Washington. The conversations were possibly illegal. Flynn and Kislyak’s communications, by phone and text, occurred on the same day the Obama Administration announced the expulsion of thirty-five Russian diplomats in retaliation for Russia’s efforts to swing the election in Trump’s favor. Flynn had previously denied talking about sanctions with the Ambassador. At the restaurant, he said that he didn’t think there was anything untoward about the call: “I’ve had a relationship with him since my days at the D.I.A.”—the Defense Intelligence Agency, which Flynn directed from 2012 to 2014. But, in a classic Washington spectacle of action followed by coverup followed by collapse, Flynn soon started backpedalling, saying, through a spokesman, that he “couldn’t be certain that the topic [of sanctions] never came up.”

He compounded his predicament by making the same denial to Vice-President Mike Pence, who repeated it on television. Flynn later apologized to Pence. But by then his transgressions had been made public. In a White House characterized by chaos and conflict—a Byzantine court led by a reality-television star, family members, and a circle of ideologues and loyalists—Flynn was finished.

The episode created countless concerns, about the President’s truthfulness, competence, temperament, and associations. How much did Trump know and when did he know it?

John McCain, a Republican and the chairman of the Senate Armed Services Committee, said that the fiasco was a “troubling indication of the dysfunction of the current national-security apparatus” and raised “further questions” about the Trump Administration’s intentions regarding Vladimir Putin’s Russia.

In one of several recent conversations, Flynn told me, “We have to figure out how to work with Russia instead of making it an enemy. We have so many problems that we were handed on a plate from this President”—meaning Obama. He lifted a bread plate and waved it. He characterized the negative attention on him as part of a larger conspiracy against Trump. “I’m a target to get at Trump to delegitimize the election,” he said. The press had him “damn near all wrong.” Reporters were just chasing after wild theories, while neglecting to consider his career as a decorated Army officer. “You don’t just sprinkle magic dust on someone, and, poof, they become a three-star general,” he said.

But, even before Flynn’s rapid fall, his closest military colleagues had been struggling to make sense of what had happened to the talented and grounded general they once knew. “Mike is inarguably one of the finest leaders the Army has ever produced,” James (Spider) Marks, a retired major general, told me. And yet, watching the first night of the Republican National Convention, last July, Marks was taken aback when his old friend appeared onscreen.

“Wake up, America!” Flynn said, his jaw set and his hands gripping the sides of the lectern. The United States was in peril: “Our very existence is threatened.” The moment demanded a President with “guts,” he declared, not a “weak, spineless” one who “believes she is above the law.”

In the early two-thousands, Marks was Flynn’s commanding officer at the Army’s intelligence academy, in Fort Huachuca, Arizona; one of his daughters went to school with one of Flynn’s sons. Marks regarded Flynn as “smart, humble, and funny.” What he saw on TV was something else: “That’s a vitriolic side of Mike that I never knew.”

When, twenty minutes into the speech, Flynn mentioned Hillary Clinton, the Convention audience responded with chants of “Lock her up!” Flynn nodded, leading the chant: “That’s right—lock her up.” He went on, “Damn right. . . . And you know why we’re saying that? We’re saying that because, if I, a guy who knows this business, if I did a tenth—a tenth—of what she did, I would be in jail today.”

Marks’s thirty-five-year-old daughter, who was watching with him, turned to her father and said, “Dad, General Flynn is scaring me.”

Trump, in his inaugural address, presented a dire image of the country—a nation suffering from poverty and blight, overextended abroad, and neglectful of its own citizens. He pledged to end the “carnage” by putting “America first”—echoing the isolationist creed of the nineteen-thirties.

The beginning of Trump’s Presidency remained true to his campaign: even when it came to the highly sensitive issues of national security, Trump and his aides acted with ideological ferocity and a heedless sense of procedure that alarmed many inside the government. The Trump Administration’s early days have invited comparison to the most unnerving political moments in memory, particularly Richard Nixon’s behavior during the Watergate scandal.

On January 27th, a week after taking office, Trump issued an executive order suspending all refugee admissions and temporarily banning entry to citizens from seven Muslim-majority countries. His chief political strategist, Stephen Bannon, reportedly oversaw the crafting of the order, along with Stephen Miller, the White House’s senior policy adviser. (Miller disputes this.) Flynn raised some concerns about how the order might affect relationships with allies, but those were ignored. James Mattis, the Secretary of Defense, and General Joseph Dunford, the chairman of the Joint Chiefs of Staff, received little notice of the order.

The next day, Trump signed another executive order, reorganizing the National Security Council. He promoted Bannon, a former investment banker and chairman of the far-right Web site Breitbart News, to a permanent seat on the “principals committee.” Elevating a political adviser to national-security policymaking marked a radical departure from the practice of recent Administrations.

By this point, the Justice Department had informed Trump officials of concerns about Flynn’s conversations with the Russian Ambassador and his public accounting of them. The acting Attorney General, Sally Yates, a holdover from the Obama Administration, told the White House that she worried Flynn might be vulnerable to blackmail by Russian agents, the Washington Post reported. Yet Flynn remained an important player in national-security matters. “He was always in the room, and on every call,” one Administration official told me.

Each morning, Flynn attended Trump’s intelligence briefing—the President’s Daily Brief. Bannon joined occasionally, as did Mike Pompeo, the director of the C.I.A., and Reince Priebus, the White House chief of staff. Flynn conferred with senior intelligence officials on how to best tailor the briefing for Trump. Presidents are particular about how they receive information, Michael Morell, a former acting C.I.A. director, who prepared and delivered the President’s Daily Brief to several Presidents, told me. George H. W. Bush preferred text on a half page, in a single column, limited to four or five pages; George W. Bush liked his briefs fifteen to twenty pages long, and preferred his briefer to stay in the room while he read the document; Barack Obama studied the material alone, over breakfast. Trump’s briefings were being shaped to address macroeconomics, trade, and “alliances,” Flynn told me, in a telephone conversation earlier this month. “The P.D.B. is not always about just your enemies.”

Congress created the National Security Council in 1947, in the hope of establishing a more orderly process for coördinating foreign and defense policy. Six years later, Dwight Eisenhower decided that the council needed a chief and named the first national-security adviser—a former soldier and banker, Robert Cutler. The position evolved into one of enormous importance. McGeorge Bundy, who served under John F. Kennedy and Lyndon B. Johnson, regarded himself as a “traffic cop”—controlling access to the President. Under Richard Nixon, Henry Kissinger dramatically expanded the role, often meeting directly with the Soviet Ambassador, and bypassing the State Department.

The temptations of power nearly overwhelmed Ronald Reagan’s Presidency, in what became known as the Iran-Contra affair, when national-security staffers were discovered to be running covert actions involving Iran and Central America. The scandal prompted some to call for the national-security adviser to become a Senate-confirmed position. Heading off these demands, George H. W. Bush chose a retired general, Brent Scowcroft, who had held the job under Gerald Ford, to return to the role, confident that Scowcroft would respect the lines between intelligence work, military operations, and policymaking. “He will be an honest broker,” Bush said.

Since then, according to Stephen Hadley, George W. Bush’s second-term national-security adviser, the “honest broker” has become the model for Republican and Democratic Administrations alike. That meant overseeing a process that is “fair and transparent, where each member of the council can get his views to the President,” Hadley said. In late November, Hadley met with Flynn, who was seeking advice, at Trump Tower. Hadley left the meeting optimistic that Flynn meant to act as a facilitator in the traditional way.

But Flynn’s challenge—and now, potentially, his successor’s—was unique, as Bannon had seemingly moved to set up a kind of “parallel, shadow” national-security staff for his own purposes, one council staffer told me. Bannon, who had no direct experience in policymaking, seized a central role on issues dear to Trump. For example, during the campaign Trump had railed against NATO members for not paying their full freight, which unnerved diplomats and politicians throughout Europe. On February 5th, according to the staffer, Bannon sent questions to the N.S.C. staff, requesting a breakdown of contributions to NATO from individual members since 1949. Many of the rank-and-file staffers were alarmed, not just because the questions seemed designed to impugn NATO’s legitimacy but because they represented a breach of protocol by tasking N.S.C. staffers with political duties. “Those were Flynn’s people, not political operatives,” the staffer said.

Flynn came into the White House wanting to streamline the bureaucracy of the N.S.C., which is staffed mostly by career civil servants from the State Department, the Pentagon, and intelligence agencies, believing that it moved too ponderously under Obama. But Flynn, in a contest for power with Bannon, soon seemed to realize that the traditional setup could help him build influence in the White House. “It was dawning on him that the process privileged him,” the N.S.C. staffer said. Others in the White House treated the customary protocols as impediments. “We are moving big and we are moving fast,” Bannon said, according to the Times.

Before Flynn’s troubles mounted, I asked him whether it was appropriate for Bannon to have a permanent seat on the N.S.C. He paused. “Well, I mean, that decision’s been made,” he said. Besides, didn’t other political advisers enjoy similar access? He brought up Valerie Jarrett, a senior adviser to Obama. Jarrett did not have a seat on the National Security Council, I said. “She didn’t? How about, like, Axelrod? He was Clinton, right?” (David Axelrod, who was Obama’s chief strategist, sometimes sat in on N.S.C. meetings but did not participate in policymaking discussions.) Look, Flynn said, “the President shapes the team that he needs to be able to do the job that he has to do. So that’s kind of where we are on that one.”

Flynn grew up in a large Irish-American household, in Middletown, Rhode Island. He was one of nine children. His father was a soldier, a veteran of the Second World War and Korea, who retired as a sergeant first class in the Army; his mother, a high-school valedictorian, worked at a secretarial school and was heavily involved in Democratic politics, before going back to school to get undergraduate and law degrees. A headstrong teen-ager, Flynn skateboarded in drained swimming pools and surfed through hurricanes and winter storms. “Mike was a charger,” Sid Abruzzi, a surf-shop owner in nearby Newport, who knew Flynn as a teen-ager, said.

In 1981, after graduating from the University of Rhode Island, Flynn joined the Army. He qualified as an intelligence officer, and got orders to join the 82nd Airborne Division, a paratrooper unit in Fort Bragg, North Carolina. In 1983, Flynn deployed to Grenada, as part of the American invasion force. He set up a listening post on a cliffside to intercept Cuban radio transmissions. One day, spotting two American soldiers being swept out to sea, Flynn leaped off the cliff—“about a forty-foot jump into the swirling waters,” he recalls, in his book, “The Field of Fight”—and rescued the men.

He won a rapid series of promotions. In 1994, he helped plan operations in support of the American invasion of Haiti. After that, he rotated to Fort Polk, Louisiana, the site of an Army base for urban-combat and special-operations training. In 2004, he deployed to Iraq with the Joint Special Operations Command, an élite counterterrorism unit composed of operators from the Delta Force, Rangers, SEAL Team Six, and others. Its culture is unusual in the military: rank is respected but not revered; sergeants challenge colonels, and colonels challenge generals. Flynn, then a colonel, in charge of the command’s intelligence collection and analysis, had ambitions for expanding the reach of special operations. He considered the command’s operators expert killers—“the best spear fishermen in the world.” But, in order to quell the insurgency spreading in Iraq, they would have to become “net fishermen,” taking down terrorist networks, he said, in a 2015 interview.

Flynn encouraged his men to think more like detectives as they hunted Al Qaeda militants; he brought F.B.I. agents in to instruct operators in how to collect and preserve evidence. A former Ranger recalled storming a house, flex-cuffing the tenants, then staying for several hours, risking exposure, while he and his teammates searched behind walls and under mattresses for a single thumb drive—which they found, eventually, in a pipe beneath the kitchen sink. Intelligence operatives would gather information by hacking militants’ computers, intercepting their phone calls, and surveilling them with drones. “We were able to mass so much information against individuals we captured that at some point they realized it was no use lying to us anymore,” Flynn says, in “Twilight Warriors: The Soldiers, Spies, and Special Agents Who Are Revolutionizing the American Way of War,” by James Kitfield.

On the afternoon of April 8, 2006, American soldiers helicoptered into Yusufiyah, a town outside Baghdad. They raided a suspected Al Qaeda safe house and detained twelve middle-aged men, who were taken to Balad Air Base, the site of the command’s Iraq headquarters, for questioning. Flynn observed some of the interviews. Over weeks of interrogation, the prisoners repeatedly denied knowing anything about Al Qaeda or its leader in Iraq, Abu Musab al-Zarqawi. Finally, two interrogators confronted one of the prisoners about a trip to Amman, Jordan, just before the devastating hotel bombings the previous year. The prisoner started talking, and divulged the identity of Zarqawi’s spiritual adviser and where to find him. Drones tracked the adviser for weeks. One day, the man came out of his house and got into a silver sedan. After two vehicle switches, he pulled into a compound in Hibhib, thirty miles north of Baghdad. A few minutes after the adviser arrived, another man emerged briefly from the house. He matched the description of Zarqawi.

As Flynn and his boss, General Stanley McChrystal, JSOC’s commander, watched on a video feed, an F-16 dropped two bombs on the house. A Delta Force squad quickly arrived at the scene and seized Zarqawi, who died soon afterward. Back at Balad, Flynn and McChrystal inspected the corpse, laid out on a tarp, confirming that it was Zarqawi.

In 2008, Flynn got a new assignment, at the Pentagon, as the senior intelligence officer reporting to the Joint Chiefs of Staff. It was an awkward fit. Flynn, now a major general, was unfamiliar with ordinary Pentagon decorum and sometimes struggled to summon the diplomacy required for the job. Intelligence officers are often irascible figures. “We are trained to be contrarians,” Marks, the retired major general, who was the senior intelligence officer during the invasion of Iraq, said. “I’m the only guy in the room who gets paid to tell you that you’re not as handsome or as smart as you think you are. I’m the one who looks the boss in the eye and says, ‘Your plan is all fucked up.’ ”

In November, 2008, Obama won the Presidency, having pledged to draw down troops in Iraq and shift military resources back to Afghanistan. He chose McChrystal to lead American forces in Afghanistan. McChrystal asked his friend Flynn to become his director of intelligence. Their collaboration in Iraq had severely crippled Al Qaeda. In Afghanistan, though, the terrain was less familiar, and their mission quite different, with a much greater emphasis on winning “hearts and minds.” Still, Flynn was thrilled to be heading to the battlefield again. According to a friend, when she asked Flynn whether he’d regret missing an almost certain promotion in Washington, he replied, “Are you kidding me? I get to go back to the shit with Stan.”

He landed in Afghanistan in June, 2009. His office was a windowless converted shipping container, and during long days he took briefings and pored over classified assessments. Flynn often ate his meals in the chow hall and chatted with subordinates. “I have no recollection of any other general officers doing that,” Toni Gidwani, an intelligence analyst who worked with Flynn in Afghanistan, told me. Flynn was intense, but he was also funny and “called bullshit when he saw it,” according to Vikram Singh, who is now at the Center for American Progress, and at the time was advising Richard Holbrooke, Obama’s chief envoy to Afghanistan and Pakistan.

Flynn’s directives, however, could at times be difficult to follow. His talent for absorbing information could race ahead of his analytical abilities. “He is not a linear thinker,” an intelligence analyst who served on multiple assignments with Flynn said. Stephen Biddle, a defense-policy fellow at the Council on Foreign Relations, recounted late-night meetings in Flynn’s container: “His ideas and assessments kept moving around.” Max Boot, a civilian adviser in Afghanistan at the time, told me that Flynn got “jerked around by the data”—he would contend that the Taliban were nearly defeated and then, with no less conviction, argue that the militant group was stronger than ever.

Part of the challenge was the shortage of reliable intelligence in Afghanistan. Flynn considered some of the C.I.A.’s activities counterproductive. When Ahmed Wali Karzai, the brother of President Hamid Karzai and a suspected drug trafficker, was revealed as a longtime C.I.A. asset, Flynn voiced his displeasure with the agency, telling the Times, “If we are going to conduct a population-centric strategy in Afghanistan, and we are perceived as backing thugs, then we are just undermining ourselves.”

Flynn dispatched a Marine Corps first lieutenant to travel around the country interviewing marines, soldiers, and civilian partners about their intelligence needs. The lieutenant, Matthew Pottinger, had been a Beijing correspondent for the Wall Street Journal before enlisting as an intelligence officer in the Marines. Throughout the autumn of 2009, Pottinger crisscrossed the country. What he heard was dispiriting. An operations officer told him that his knowledge of what was happening in villages was “no more than fingernail deep.” The Americans were ignorant of local power brokers, religious practices, and economics. Pottinger, Flynn, and a senior official from the Defense Intelligence Agency compiled their observations, along with recommendations for changes, into a damning report.

In late December, Flynn e-mailed the report to dozens of colleagues at the Pentagon, the White House, and the C.I.A. The response was underwhelming; most didn’t even bother to reply. Pottinger suggested finding a publisher outside the government, and Flynn agreed. On January 4, 2010, the Center for a New American Security, a progressive think tank, released “Fixing Intel: A Blueprint for Making Intelligence Relevant in Afghanistan.” Reviews outside the military were laudatory, but senior Pentagon and C.I.A. officials were angered by Flynn’s decision to go public. “I was very concerned about an intelligence officer openly criticizing our intelligence community,” former C.I.A. director Leon Panetta told me. Flynn and Pottinger understood that they might be fired.

Defense Secretary Robert Gates delivered a judgment of the report that saved them. He called it “exactly the type of candid, critical self-assessment” that the military needed. “Fixing Intel” consolidated Flynn’s exalted status in the intelligence community. In 2012, Defense News ranked him seventeenth on its “100 Most Influential” list, heralding the report as something that “might have ended his career” but which, instead, “accelerated it.”

In April, 2012, Obama nominated Flynn to be the director of the Defense Intelligence Agency. Within the intelligence community, the agency was considered a backwater. “It’s the bastard child,” Mary Beth Long, the former C.I.A. officer, said. The agency, whose headquarters are in southwest Washington, produced reports on topics like Middle Eastern weapons deals, changes of command in China, and troop movements on the Korean peninsula—essential work for assessing foreign military capabilities but hardly exciting.

To invigorate the D.I.A., Flynn wanted to break down the barriers between collectors and analysts; enhance the stable of clandestine case officers who operated overseas, like their C.I.A. counterparts; and reorganize the agency on the basis of geography. The goal was to transform the D.I.A. into a more agile organization.

Flynn’s ideas were informed by his experience in helping to overhaul JSOC. But it was unclear whether they would work at the D.I.A., with seventeen thousand employees. “JSOC has a small, tight-knit group of folks making real-time tactical decisions that must be executed tonight,” a senior military intelligence official told me. “A big organization like the D.I.A. just can’t respond that quickly.”

Peter Shelby, a retired marine and former D.I.A. official, told me he assumed that Flynn would be methodical in his approach: spend a few months at headquarters; learn how the organization worked; cultivate respected agency veterans; and then introduce changes. Instead, Shelby said, “Flynn came in and threw a bomb to explode the whole place, and then just let the dust settle.”

Employees started to complain. Many sought reassignment with other agencies. “Morale was in the toilet,” Shelby said. “To higher-level observers, Flynn looked like this bold leader, willing to make changes in the face of opposition. But, the further down you went, the more negative impact there was, because it was complete chaos.”

Moreover, Flynn could be sloppy with numbers and details—misstatements that his staffers derided as “Flynn facts.” His habit of chasing hunches also exasperated some staff members. In September, 2012, after the terrorist attack on the U.S. consulate and annex in Benghazi, Flynn urged an investigation into an Iran connection; his insistence that Iran was involved “stunned” subordinates, according to the Times. (Flynn denies that he asked for a probe.) An intelligence analyst who worked with Flynn during this period told me that his iconoclasm sometimes went too far. “By nature, Flynn takes a contrarian approach to even the most simple analytic issues,” the analyst said. “After Benghazi, I remember him using the phrase ‘black swan’ a lot. What’s a ‘black swan’? He was looking for the random event that nobody could predict. Look, you certainly have to keep your eye on the ball for that, but there’s a reason why it’s a black swan. You shouldn’t dedicate a ton of time to that.”

In 2013, Flynn arranged a trip to Moscow to speak to a group of officers from the G.R.U., Russia’s intelligence agency, about leadership development. His decision to go was a controversial one. Flynn believed that there were opportunities to find common ground with Russia. But Steven Hall, the C.I.A.’s chief of Russia operations at the time, was skeptical. “He wanted to build a relationship with his counterparts in the G.R.U., which seemed, at best, quaint and naïve,” Hall told me. “Every time we have tried to have some sort of meaningful coöperation with the Russians, it’s almost always been manipulated and turned back against us.”

Several months after Flynn returned from his Moscow trip, he hoped to reciprocate by inviting several senior G.R.U. officers to the United States. Clapper, the director of national intelligence, cautioned him against it. Russia had recently annexed Crimea, and Russian special-forces operatives were fomenting a violent clash between rebels and Ukrainian troops in eastern Ukraine.

By then, Flynn had become a target of scorn for many inside the department. His deputy, David Shedd, became one of his harshest critics, and did little to hide his disdain. “I was walking by the front office once and heard David Shedd say, ‘I’m going to save the agency from the director,’ ” Simone Ledeen, who works in counter-threat finance at a multinational bank, said. Ledeen had worked for Flynn in Afghanistan, at the office for the director of national intelligence, and in the D.I.A., doing threat-assessment research. (She is also Michael Ledeen’s daughter.)

Normally, a D.I.A. director serves for three or more years, but, in late 2013, Clapper and Michael Vickers, the Under-Secretary of Defense for Intelligence, were concerned about the tumult inside the agency and told Flynn that his tenure would last just two years. Flynn unsuccessfully tried to extend his term when his successor’s nomination was delayed. Shedd later became the acting director.

On August 7, 2014, at a ceremony in the atrium of the D.I.A.’s headquarters, Flynn retired from the military, after thirty-three years. His wife and two sons attended, as did Michael Ledeen. The senior military intelligence official, who was present, told me that Flynn was obviously bitter: “He was loading up, and he was not going to go quietly.”

Flynn, who was fifty-five, began fashioning a post-military life. He started his own business, the Flynn Intel Group, which offered clients a range of private intelligence and security services. He did some freelance consulting and also worked with SBD Advisors, a strategic consulting firm whose roster included the former chairman of the Joint Chiefs of Staff Admiral Michael Mullen; former chief of the Special Operations Command Admiral Eric Olson; and other retired military officers. In January, 2015, Flynn signed with Leading Authorities, a speakers’ bureau, which promoted his expertise in leadership, cybersecurity, and terrorism.

Flynn began developing a public profile as a decorated former general with experience in fighting Islamic extremism. A month later, he made an appearance on “Charlie Rose.” He spoke at length about the threat posed by the Islamic State, which had been executing hostages and rapidly acquiring territory in northern Iraq and Syria. But America faced bigger foes than isis, he said. “Iran has killed more Americans than Al Qaeda has through state sponsors, through its terrorist network, called Hezbollah.”

This was a puzzling assertion. “Hezbollah has killed more Americans than Al Qaeda?” Rose asked.

Flynn began a count, starting with Hezbollah’s 1983 bombing of the Marine barracks in Beirut that killed two hundred and eighty-three people. He cited other instances, but his math made little sense, and the numbers fell far short of the nearly three thousand killed by Al Qaeda’s attacks on 9/11.

Rose moved on, but a friend who had accompanied Flynn to the studio pulled him aside after the taping and questioned his Iran claim. One of Rose’s producers offered to fact-check the segment, but he waved off the suggestion. Another friend who’d come to the taping suggested contacting an expert from the intelligence community. That wouldn’t be necessary, Flynn said—he would just call Michael Ledeen.

Flynn and Ledeen’s relationship soon became a professional collaboration. Flynn asked Ledeen to help him write a book. Flynn wanted to position himself as a sage counsellor for the upcoming Presidential campaign. Ledeen had written more than a dozen books, including five on Iran. They were often polemical works, with titles such as “The War Against the Terror Masters” and “The Iranian Time Bomb,” and were filled with sweeping statements like “Islamic fundamentalism, of which the ideology of the Iranian regime is a textbook case, draws much of its inspiration from Mussolini, Hitler, and Stalin.”

In April, 2015, Flynn accepted an invitation to spend a week at Dartmouth. Daniel Benjamin, a former State Department counterterrorism chief who now directed the school’s international-affairs center, had come to know Flynn in Afghanistan. He considered him friendly and engaging, and thought students and faculty would appreciate his insights and his unconventionality. He set up class visits, dinner discussions, and a talk, which Flynn titled “World Without Order.”

Benjamin told me that he quickly realized during the visit that Flynn’s “easygoing pragmatism” had given way to some “very hard-edged ideas,” particularly on Iran. Flynn voiced contempt toward Iran’s leaders (“They are liars”) and said that they had “no right” to participate in negotiations with the United States over their nuclear program. (The Iran nuclear deal was signed in July, 2015.)

“I’ve encountered plenty of military officers who were deeply upset by the role that Iranian-backed militias played in Iraq, but Flynn’s animosity was off the charts,” Benjamin said. Flynn expressed similarly harsh views of Islam in general, describing the faith as a political ideology, and not a religion. Benjamin, who, in 2002, co-wrote a book, “The Age of Sacred Terror,” about the ideological war that America faced against radical Islam, deemed Flynn’s comments “pointlessly pejorative” and thought they would serve only to inflame extremists. He began discouraging Dartmouth’s administrators and faculty from attending the events.

On Fox News, NBC’s “Meet the Press,” CNN, and elsewhere, Flynn became increasingly critical of the Obama Administration. He lashed out at the Iran nuclear deal, the Administration’s ISIS strategy, and its approach to radical Islam generally. Several Republican hopefuls preparing to run against Hillary Clinton asked for his advice. Carly Fiorina, the former Hewlett-Packard chief executive, brought Flynn on as an informal adviser for her Presidential bid. She told me that she found him refreshing. “He is a very down-to-earth, approachable guy,” she said. She was also impressed by his candor. Flynn, she said, “doesn’t pull punches.”

In August, 2015, Flynn went to New York to meet Trump for the first time. They were scheduled to talk for thirty minutes; the conversation lasted ninety. Flynn was deeply impressed. “I knew he was going to be the President of the United States,” he told me.

Two months later, Flynn appeared on RT, the English-language Russian television channel, formerly known as Russia Today. The outlet was widely regarded as a propaganda arm of the Kremlin, even before a recent U.S. intelligence report on Russian hacking and the Presidential election said that the channel had become an important part of a “Kremlin-directed campaign to undermine faith in the US Government.” Flynn discussed the civil war in Syria, where Russian jets were flying bombing sorties in support of President Bashar al-Assad’s regime. He contrasted Putin’s resolve with what he described as Obama’s dithering in the region: “There’s no coherence or no clarity to the strategy.”

In early November, 2015, a D.C.-based representative of RT contacted Flynn’s speakers’ bureau and invited him to Moscow for the channel’s tenth-anniversary celebration. The fee was approximately forty thousand dollars, according to a source familiar with the arrangement. This trip was considerably more fraught than the one he had made as D.I.A. director. On December 1st, RT issued a press release announcing Flynn’s participation. In e-mails, Simone Ledeen urged her former boss, and family friend, to reconsider. “I begged him, ‘Please, sir: don’t do this. It’s not just you. You’re a retired three-star general. It’s the Army. It’s all of the people who have been with you, all of these analysts known as “Flynn’s people.” Don’t do this to them. Don’t do this to yourself.’ ”

Flynn assured his critics that he knew what he was doing. “Know my values and beliefs are mine & won’t change because I’m on a different piece of geography,” he tweeted. Before the trip, Flynn received a classified counterespionage briefing at D.I.A. headquarters. Hall, the former C.I.A. chief of Russia operations, told me, “Whatever personal electronic device you carry with you into Russia will be compromised.”

Flynn stayed at a hotel near Red Square. The RT gala featured speakers and panel discussions during the day and a dinner at night. That morning, Sophie Shevardnadze, an RT correspondent, interviewed Flynn. From the stage, he confessed to feeling as if he were behind enemy lines. “I’m sort of in the lair,” he said.

A Russian jet had recently been shot down near the Syrian border by a Turkish plane, and Shevardnadze asked Flynn how Russia should respond. “Are we not to react? What does Turkey expect?” she asked. Circumspect, Flynn said, “I don’t know what Turkey expects. I don’t know what Russia expects.”

Flynn also seemed to go out of his way to tweak the Russian government and its partners in Damascus and Tehran. “Let’s face it, come on, is Assad the future of Syria, given the way the situation has unfolded?” Flynn said. He added that Assad’s allies in Iran were making things worse in Syria and elsewhere. “Iran exports a lot of terrorism,” he declared.

Flynn was seated at the head table for dinner that evening. Putin sat to his left. Cyril Svoboda, the former foreign minister of the Czech Republic, sat to Flynn’s right. I called Svoboda, who speaks fluent English and Russian, and who translated a brief exchange between the two men, and asked what they discussed. “It was very, very short,” Svoboda said. “ ‘Kak vashi dela?’ ‘Shto novovo?’ ‘Khorosho.’ ” (“How are you?” “What’s new?” “Good.”)

After dinner, Putin went onstage and congratulated RT on its success. The Russian government wasn’t perfect, he said, so he appreciated RT for its presentation of “various points of view.” After Putin concluded his remarks, Flynn, joining other diners, stood and applauded.

Last year, Flynn talked to Dana Priest, of the Washington Post, about the trip. When Priest asked why he would go on RT, a state-run channel, Flynn replied, “Well, what’s CNN?”

“Well, it’s not run by the state,” Priest said. “You’re rolling your eyes.”

“Well, what’s MSNBC?” Flynn said. “I mean, come on . . . what’s Al Jazeera?”

By early 2016, Flynn was enthusiastic about Trump. “He picked the right horse and he picked it early,” the close Flynn associate told me. Flynn’s Twitter feed, which had once been full of sunset photos and surf reports, turned increasingly reactionary, particularly on immigration and Islam. “Fear of Muslims is RATIONAL,” he posted, last February. Not long afterward, he retweeted a picture apparently showing refugees tromping across the European countryside with text that read, “Historians will look back in amazement that the West destroyed its own civilization.”

In July, his book with Ledeen, “The Field of Fight: How We Can Win the Global War Against Radical Islam and Its Allies,” came out. After Trump tweeted an endorsement, the book made the Times best-seller list. Although Ledeen’s name appears (in small type) on the cover, “The Field of Fight” is written in the first person and presented in Flynn’s voice. But I ran the book through software that allowed me to compare it to the text of Ledeen’s previous books and articles. Dozens of matches turned up. The similarities suggested just how much Ledeen’s long-standing obsessions had melded into Flynn’s. Although an ISIS flag is pictured on the front cover, “The Field of Fight” is, in many ways, a call to action against Iran. “Every day we see evidence of Iranian espionage in the United States,” Flynn writes. “It is hard to imagine that there are no Hezbollah terrorist groups inside this country. If they could blow up buildings in Buenos Aires, they can surely do the same here.”

During the summer of 2016, the Trump campaign floated Flynn, a lifelong Democrat, as a Vice-Presidential candidate. After the Republican Convention, Flynn became a regular presence at Trump campaign events, sometimes accompanied by his older son, Michael, Jr. Flynn had been absent for long stretches of Michael, Jr.,’s, teen-age years and early adulthood—he reportedly missed his wedding while deployed in Iraq. Flynn made Michael, Jr., his chief of staff.

In part through his son, Flynn began flirting with an online community of conspiracy theorists and white nationalists who referred to themselves as the “alt-right.” The neo-Nazis among them called Trump the “God Emperor.” On Twitter, Flynn frequently tagged Mike Cernovich, an alt-right activist, in tweets, and encouraged others to follow his feed. Michael, Jr., promoted stories from Alex Jones, the right-wing radio host who believes that the 9/11 attacks, and the 2012 school shooting in Sandy Hook, were inside jobs. A little more than a year ago, Michael, Jr., tweeted @billclinton, “You’re a Rapist.”

Flynn’s own views seemed to be tilting increasingly toward the fringe. He, as Trump has, publicly insinuated that Obama was a secret Muslim, and not a true American. “I’m not going to sit here and say he’s Islamic,” Flynn said of Obama, during remarks last year before the American Congress for Truth, an anti-Muslim group. But Obama “didn’t grow up an American kid,” Flynn said, adding that the President’s values were “totally different than mine.”

Flynn also stoked fear about Muslims and, in a tweet that used the hashtag #NeverHillary, shared an anti-Semitic comment that read, in part, “Not anymore, Jews. Not anymore.” (He subsequently deleted the tweet, calling it “a mistake.”) “I’m not perfect. I’m not a very good social-media person,” he told me in one of our conversations. Stanley McChrystal and Mike Mullen, the former chairman of the Joint Chiefs, both contacted Flynn and tried, unsuccessfully, to get him to tone it down.

Flynn predicted a Trump win, but he was making contingency plans. He began reorienting his firm, the Flynn Intel Group, so that it would be able to compete for lobbying clients after the election. The firm arranged to work with Sphere Consulting, a public-relations and lobbying business in Washington.

In August of last year, a Turkish businessman with close ties to the government of Recep Tayyip Erdo?an hired Flynn Intel Group on a lobbying contract to help promote the view that Turkey’s business climate was a positive one. This was a challenging task, given that Erdo?an had survived a coup attempt just the month before, and was, in retaliation, rounding up anyone considered insufficiently faithful to his regime. Flynn had previously been critical of Erdo?an, whom he viewed as an Islamist threat. He put those concerns aside now as he vouched for Erdo?an’s government, writing an op-ed for The Hill that heralded Turkey as “our strongest ally” against ISIS.

Flynn remembered Election Night fondly, a moment of triumph. “I like to think that I helped get Donald Trump elected President,” he told me. “Maybe I helped a little, maybe a lot.” One of Trump’s first major decisions was to appoint Flynn his national-security adviser, calling him “an invaluable asset to me and my Administration.” Flynn told me, “Service was something our family was always encouraged to do.” He went on, “I made some mistakes, but I’m still serving. It’s like being a priest, you know. I’ve been called to serve.”

After the election, Flynn spent his days at Trump Tower, down the hall from Bannon and Reince Priebus. “My sched is so tight, literally from sunrise to well past sunset,” Flynn wrote me, in a text message. He was “consumed with reading.”

The team he assembled drew heavily from his former military colleagues, but the qualifications of others were less apparent. K. T. McFarland, until recently a Fox News analyst, became his deputy. Flynn’s son, Michael, Jr., did a brief stint on the transition, before he was dismissed, after continuing to push on Twitter the fake-news story about Hillary Clinton’s role in a child-sex-trafficking ring in a pizzeria in northwest Washington, D.C.

Michael Ledeen volunteered to help Flynn by examining Obama’s executive orders on foreign policy, particularly on Iran, recommending “which ones should be cancelled, which ones should be expanded, and so on.” Ledeen considered the moment an auspicious one. “I’ve been agitating for thirty years to go after Iran,” he said. “Now all of a sudden we’ve got a national-security adviser, a Secretary of Defense, and the head of the C.I.A. who all agree.”

Like Trump, Flynn stewed over what was said, and written, about him. Much of it was unfavorable. A scathing Times editorial called his appointment “alarming,” saying that he “would encourage Mr. Trump’s worst impulses.” The editorial went on, “A core theme of Mr. Trump’s campaign was making America safer. With this appointment, he is doing the opposite.”

When we met at the restaurant before the Inauguration, Flynn was guarded. “What’s the purpose of this thing?” he asked me. He had previously questioned whether I would “rehash all this stuff about me being anti-Semitic and pro-Russia and an Islamophobe.”

Flynn told me he prided himself as a strategist. I asked about his strategy for combatting ISIS. He said that Obama had “too narrowly defined” efforts to defeat the enemy. Part of the Trump Administration’s military strategy should include “fighting these guys on the battlefield,” he told me.

Although Bannon’s clout seemingly grew by the day, Flynn’s imprint on national-security policy was unmistakable. Traditionally, the measure of a national-security adviser’s effectiveness has been defined by his relationship with the President. That may well have enabled Flynn to hold on to his job as long as he did; Trump’s loyalty is well known. (When I asked Flynn if he regarded himself as the “honest broker,” he said that model was a “misnomer” with Trump. “The honest broker? It’s Donald Trump.”)

Nine days into the new Administration, Iran test-fired a ballistic missile from a remote base in the desert. Flynn regarded the test as a violation of U.N. Security Council Resolution 2231, covering the agreement on Iran’s nuclear program. (In fact, the resolution does not prohibit Iran from firing missiles but, rather, calls upon Iran “not to undertake any activity related to ballistic missiles designed to be capable of delivering nuclear weapons.”)

Flynn’s team drafted a strongly worded warning that criticized the Obama Administration for “fail[ing] to respond adequately to Tehran’s malign actions.” The White House sent a draft to the Pentagon for review. According to a senior military official, staffers in the Defense Secretary’s office recommended softening some of the language and removing the condemnations of the Obama Administration. Their suggestions were ignored.

Three days after the missile test, Sean Spicer, the White House press secretary, interrupted his daily briefing and invited Flynn to the lectern. The Times had just published a story describing Flynn’s influence as waning, and he seemed intent on proving otherwise. Trump had encouraged him to read the statement himself, Flynn later told me. The President “felt a strong message needed to be put out,” he said, as if he could dispel rumors of White House turmoil by threatening war overseas.

Flynn scolded Iran for its “destabilizing behavior across the entire Middle East” and declared, “As of today, we are officially putting Iran on notice.” I spoke to Flynn a few days later. I asked him what he meant by “on notice.” He replied, “We have a standard, set by sanctions that have been put in place, that we expect they will meet.” I asked if he thought there were ways to modify Iran’s behavior short of regime change.

“You’ll have to ask Khomeini,” he said. Ayatollah Ruhollah Khomeini, the cleric who led the Islamic Revolution, died in 1989. Did Flynn mean Ayatollah Ali Khamenei, who has led the country since then?

“Come on,” Flynn said. “That’s my Irish brogue.” He declined to specify how Iran might be punished, because he didn’t want to “telegraph” military action. “One thing I learned as a lieutenant in the Army is that the best plan is the one that gives you the most options at the last possible minute,” he said.

Military officials have been drawing up retaliatory options, including warplanes, drones, troops, and cyberattacks. “Planning is trying to keep up with the rhetoric,” one senior defense official told me.

The end for Flynn came rather abruptly. He had spent the weekend with the President and the Prime Minister of Japan at Mar-a-Lago, Trump’s resort in Palm Beach, Florida, where they had used a table in an open dining area as an impromptu—and unsecured—situation room after a ballistic missile test by North Korea. But, back in Washington on Monday afternoon, there was confusion about Flynn’s standing. During a television interview, Kellyanne Conway, a senior White House adviser, said that Flynn enjoyed Trump’s “full confidence.” Then, within the hour, Spicer said that Trump was “evaluating the situation.” Flynn went about his duties as usual that afternoon, participating in foreign-policy discussions in the Oval Office, an Administration official told me.

But, that evening, another Post article appeared online, this time about the Justice Department’s blackmail fears. Soon afterward, Trump asked for Flynn’s resignation. The news broke just before eleven.

Since the election, Flynn had been “read in” to dozens of “special access programs,” the country’s most highly classified intelligence operations. By protocol, he would have spent his final moments in the White House being “read out” of each program, a process that involves signing multiple confidentiality forms. At around 11:30 p.m., he walked out of the White House and called his wife.

At that hour, the roads were empty and Flynn drove, alone, to his home, in Old Town Alexandria. He barely slept that night. On Tuesday, a government representative came to his home to collect his phones, badges, and keys. He spent the next few days with his wife, taking long walks, “reflecting and capturing his thoughts,” the close associate told me. As Washington, just across the Potomac River, convulsed, Flynn was going through his own “range of emotional swings,” the associate said.

Last Wednesday, at a midday press conference, Trump, who Spicer said earlier had lost trust in Flynn, now praised him (“a fine person”), blamed the media for his ouster (“The press should be ashamed of themselves”), and attributed Flynn’s resignation not to potentially criminal contacts with the Russian Ambassador but to “illegal” leaks.

There were reports of investigations on an array of fronts: an F.B.I.-led inquiry into Flynn’s communications with the Russian Ambassador; an Army-led one into payments that Flynn might have received from the Russian government when he went to Moscow in 2015; and calls for probes from members of the Senate and House intelligence committees.

Flynn has been consulting with a lawyer. It is illegal for unauthorized private citizens to conduct diplomacy with foreign governments, but such a violation would be difficult to prosecute. When, soon after Flynn became national-security adviser, F.B.I. agents questioned him, he denied discussing sanctions with Kislyak, the Post reported. If he lied to the F.B.I., he could be vulnerable to felony charges.

Russian officials deny any improper contact with Flynn or anyone else in Trump’s circle. The predominant view in the state media and among Russian analysts is that the Flynn affair, coupled with the American intelligence report on the hack of the Democratic National Committee, is likely to limit Trump’s ability to make some of the major changes in U.S.-Russia policy that he was hinting at throughout the campaign.

Last week, Adam Schiff, the ranking Democrat on the House intelligence committee, along with House Minority Leader Nancy Pelosi, requested a briefing from the director of national intelligence on Flynn’s contacts with Russian officials, including unredacted transcripts of conversations. Schiff expressed concern to me about evidence preservation; the Administration had already shown its capacity for deceit. After all, he said, Trump had known “for weeks” that Flynn was lying. “The fact that they were O.K. with that tells you a lot about their comfort level misleading the public.”

A former C.I.A. official raised similar concerns about how long Flynn was allowed to stay in his job. “We’ve now got a guy briefed on our most closely guarded secrets about a whole host of issues—including Russia—who has been canned,” the official said. “We don’t have something from the movies where you can put an eraser on someone’s head and it all goes away. We’ve got to rely on Mike Flynn to keep those secrets, just as we rely on others who’ve been given access to classified information when they leave those positions.”

White House officials portrayed Flynn as having had his conversations with the Russian Ambassador on his own. But Schiff and others are doubtful. Schiff said he thought that it would be “extraordinary” if Flynn was “some kind of free agent, entering into discussions with the Russians about undermining President Obama’s sanctions against Russia for its interference in our elections to help elect Donald Trump.” (During a news conference last Thursday, Trump said that Flynn had done nothing wrong in his discussions with the Russian envoy. “I didn’t direct him,” Trump said, “but I would have directed him if he didn’t do it.”)

Some of Flynn’s former military colleagues, even those from whom he’s drifted apart in recent years, told me they were skeptical that Flynn would have conducted shadow diplomacy on his own. Despite his reputation as an agitator, he was, in the end, a soldier who followed orders, they said.

“This story is bigger than Mike Flynn,” the senior military intelligence official said. “Who told Mike to go do this? I think somebody said, ‘Mike, you’ve got some contacts. Let them know it’s gonna be all right.’ Mike’s a soldier. He did not go rogue.” ?

An earlier version of this article incorrectly stated that President George W. Bush had his daily briefing read aloud to him. The briefer presented President Bush with fifteen to twenty pages of material, but did not read them to him.

Original article here.