Many of those who observed the general’s time at the agency described him as someone who alienated both superiors and subordinates with his sharp temperament, his refusal to brook dissent, and what his critics considered a conspiratorial worldview.
Those qualities could prove problematic for a national security adviser, especially one who will have to mediate the conflicting views of cabinet secretaries and agencies for a president with no experience in defense or foreign policy issues. Traditionally, the job has gone to a Washington veteran: Condoleezza Rice, for instance, or Thomas E. Donilon.
The Last Word
The new job will give Mr. Flynn, 57, nearly unfettered access to the Oval Office. Whether it is renewed bloodletting in Ukraine, a North Korean nuclear test or a hurricane swamping Haiti, he will often have the last word with Mr. Trump about how the United States should react.
For Mr. Flynn, serving as the president’s chief adviser on defense and foreign policy matters, represents a triumphal return to government after being dismissed as agency director in 2014 after two years there.
Heading the agency, the Pentagon’s intelligence arm, was supposed to be the capstone of a storied career. Through tours in Iraq and Afghanistan, Mr. Flynn had built a reputation as a brash and outspoken officer with an unusual talent for unraveling terrorist networks, and both his fiercest critics and his outspoken supporters praise his work from those wars.
In numerous interviews and speeches over the past year, Mr. Flynn, who did not respond to request for comment for this story, has maintained that he was forced out as director for refusing to toe the Obama administration’s line that Al Qaeda was in retreat. The claim has made the general something of a cult figure among many Republicans.
“D.I.A. has always been a problem child and it remains that way,” said Rep. Devin Nunes, the California Republican who is chairman of the House Intelligence Committee and a member of Mr. Trump’s transition team. “Flynn tried to get in there and fix things and he was only given two years until they ran him out because they didn’t like his assessment.”
The congressman added: “They didn’t have an excuse to fire him, so they made it up. Nobody has been able to fix that place.”
But others say he was forced out for a relatively simple reason: He failed to effectively manage a sprawling, largely civilian bureaucracy.
At the agency, “Flynn surrounded himself with loyalists. In implementing his vision, he moved at light speed, but he didn’t communicate effectively,” said Douglas H. Wise, deputy director from 2014 until he retired in August. “He didn’t tolerate it well when subordinates didn’t move fast enough,” he said. “As a senior military officer, he expected compliance and didn’t want any pushback.”
The Boss Is Always Right
Founded in 1961, the agency has long been in the shadow of the Central Intelligence Agency, and with the end of the Cold War it lost its primary mission of collecting and analyzing information about the Soviet military. Strained by a decade of conflict in Afghanistan and Iraq, it was performing an uncertain role within the constellation of American spy agencies when Mr. Flynn arrived at headquarters in mid-2012.
The agency’s system of human intelligence collection was perceived as largely broken. The effort to rebuild it was already underway by the time Mr. Flynn took control in 2012, but he made it immediately known that he had a dim view of the agency’s recent performance.
During a tense gathering of senior officials at an off-site retreat, he gave the assembled group a taste of his leadership philosophy, according to one person who attended the meeting and insisted on anonymity to discuss classified matters. Mr. Flynn said that the first thing everyone needed to know was that he was always right. His staff would know they were right, he said, when their views melded to his. The room fell silent, as employees processed the lecture from their new boss.
Current and former employees said Mr. Flynn had trouble adjusting his style for an organization with a 16,500-person work force that was 80 percent civilian. He was used to a strict military chain of command, and was at times uncomfortable with the often-messy give-and-take that is common among intelligence analysts.
Some also described him as a Captain Queeg-like character, paranoid that his staff was undercutting him and credulous of conspiracy theories.
At times, the general also exhibited what a number of officials described as tone-deafness on the larger strategic challenges confronting the nation.
The most glaring example came in early March 2014, just after Russia had seized Crimea. American officials were weighing whether to impose sanctions in response, but Mr. Flynn was pushing ahead with plans to travel to Moscow to build on an existing intelligence-sharing initiative with his Russian counterparts. He also wanted to invite Russian military intelligence officials to Washington to discuss the threat of Islamist militants. His superiors ordered both canceled.
By the end of his tenure, he had largely cut out senior staff members from significant decision-making, relying instead on a small circle of trusted advisers he had come to know during his overseas military deployments.
His bosses — Michael G. Vickers, the under secretary of defense for intelligence, and James R. Clapper, the director of national intelligence — came to think that the agency was adrift, and that Mr. Flynn refused to address its biggest problems.
“Regrettably, he got engaged in an increasingly bitter and organizationally paralyzing feud with his senior staff when he should have been focused on building the intelligence capabilities” of the agency, said Mr. Vickers, who was Mr. Flynn’s immediate boss at the Pentagon.
During his tour in Iraq, he served under Gen. Stanley A. McChrystal, running intelligence for the military’s Joint Special Operations Command, whose relentless campaign of raids and airstrikes hollowed out Al Qaeda in Iraq. When General McChrystal went to run the war in Afghanistan in 2009, Mr. Flynn signed on as his intelligence chief.
“He wasn’t a staid intelligence officer. He was aggressive. He was about the mission,” said Richard M. Frankel, a former senior F.B.I. official who worked with Mr. Flynn at the Office of the Director of National Intelligence. “He can have sharp elbows because he is about the mission.”
He burnished his reputation as an intelligence officer — but also for controversy. He co-wrote a paper, “Fixing Intel,” that offered an early hint of his disdain for the civilian intelligence analysts he would later clash with at the agency. Published by a Washington think tank, it bluntly stated that “the U.S. intelligence community is only marginally relevant to the overall strategy,” infuriating officials at the D.I.A. and the C.I.A.
More problematic from the military’s perspective was Mr. Flynn’s willingness to share intelligence with other countries. He returned to Washington at the end of 2010, and found himself under investigation for sharing sensitive data with Pakistan about the Haqqani network, arguably the most capable faction of the Taliban, and for providing highly classified intelligence to British and Australian forces fighting in Afghanistan.
His superiors eventually concluded that he was trying to prod Pakistan to crack down on the Haqqanis (they have yet to do so), and the general remains unapologetic about sharing intelligence with British and Australian forces. “They’re our closest allies! I mean, really, we’re fighting together and I can’t share a single piece of paper?” he said in an interview last year.
Around the same time, he was also getting to know Michael A. Ledeen, a controversial writer and former Reagan administration official. The two men connected immediately, sharing a similar worldview and a belief that America was in a world war against Islamist militants allied with Russia, Cuba and North Korea. That worldview is what Mr. Flynn came to be best known for during the presidential campaign, when he argued that the United States faced a singular, overarching threat, and that there was just one accurate way to describe it: “radical Islamic terrorism.”
He has posted on Twitter that fear of Muslims is rational, written that Islamic law is spreading in the United States, and said that Islam itself is more like a political ideology than a religion. The United States, he wrote in “Field of Fight,” a book about radical Islam he co-wrote with Mr. Ledeen, is “in a world war, but very few people recognize it.”
Mr. Flynn saw the Benghazi attack in September 2012 as just one skirmish in this global war. But it was his initial reaction to the event, immediately seeking evidence of an Iranian role, that many saw as emblematic of a conspiratorial bent. Iran, a Shiite nation, has generally eschewed any alliance with Sunni militants like the ones who carried out the attack on the American diplomatic compound.
For weeks, he pushed analysts for evidence that the attack might have had a state sponsor — sometimes shouting at them when they didn’t come to the conclusions he wanted.
The attack, he told his analysts, was a “black swan” event that required more creative intelligence analysis to decipher.
“To ask employees to look for the .0001 percent chance of something when you have an actual emergency and dead Americans is beyond the pale,” said Joshua Manning, an agency analyst from 2009 to 2013.
Beyond Benghazi, American officials said that in time, the general grew angrier at what he saw as the Obama administration’s passivity in dealing with worldwide threats — from Sunni extremist terrorism to Iran. He also saw the C.I.A., an organization he had long disdained, as overly political and too willing to advance the White House’s agenda.
In particular, he became convinced that the C.I.A. was refusing to declassify many of the documents found at Osama bin Laden’s compound in Abbottabad, Pakistan, because they seemed to undercut the administration’s narrative about Qaeda strength at the time Bin Laden was killed.
“If they put out what we knew, then the president could’ve not said, in a national election, Al Qaeda’s on the run and we’ve killed Bin Laden,” Mr. Flynn said before the latest election, referring to Mr. Obama’s 2012 re-election bid. “Even today, he talks about Bin Laden as though that was a stroke of genius. I mean, c’mon!”
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