“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 Defense Intelligence 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.”