Dana Priest writes: The first time I met Michael Flynn, whom President-elect Donald Trump tapped last week to be his national-security adviser, he was wearing the Army’s weekend uniform — a baggy polo shirt and khaki pants — and swinging his Blackberry around like a cowboy would his revolver. It was the late summer of 2008, at a Washington cocktail party hosted by Flynn’s boss, Admiral Michael Mullen, who was then the chairman of the Joint Chiefs of Staff. Flynn was Mullen’s top intelligence guy.

“Look at this!” Flynn said, holding up his phone so that I could see the screen. At his request, his communications staff would send him the daily dispatches published by tribal media outlets in Pakistan’s troublesome northwest region. These articles chronicled skirmishes, feuds, and revenge killings — it was unfiltered information that any decent Western news stringer would know how to read, but that, seven years into the war in Afghanistan, the American military was still far from absorbing. Flynn got it, though. He was drawn to the little flecks of truth scattered on the ground.

A lot of reporters and other civilians found Mike, as everyone called him, refreshing. A plucky Irish Catholic kid from Rhode Island, he wasn’t impressed by rank. He told his junior officers to challenge him in briefings. “You’d hear them say, ‘Boss, that’s nuts,’ ” one former colleague said. The colleague asked not to be named, as did others I talked to for this story, either because they wanted to maintain a positive relationship with Flynn or because they did not want to criticize the incoming Administration. “When he would walk in a room, they would look up like little dogs. They just loved him.”

Flynn broke rules he thought were stupid. He once told me about a period he spent assigned to a C.I.A. station in Iraq, when he would sometimes sneak out of the compound without the “insane” required approval from C.I.A. headquarters, in Langley, Virginia. He had technicians secretly install an Internet connection in his Pentagon office, even though it was forbidden. There was also the time he gave classified information to NATO allies without approval, an incident which prompted an investigation, and a warning from superiors. During his stint as Mullen’s intelligence chief, Flynn would often write “This is bullshit!” in the margins of classified papers he was obliged to pass on to his boss, someone who saw these papers told me.

The greatest accomplishment of Flynn’s military career was revolutionizing the way that the clandestine arm of the military, the Joint Special Operations Command (jsoc), undertook the killing and capture of suspected terrorists and insurgents in war zones. Stanley McChrystal, Flynn’s mentor, had tapped him for the job. They were both part of the self-described “Irish mafia” of officers at the Fort Bragg Army base, in North Carolina. In Afghanistan and Iraq, Flynn ordered jsoc commandos to collect and catalogue data from interrogations, captured electronic equipment, pocket trash — anything that could yield useful information. By analyzing these disparate scraps of intelligence, they were able to discover that Al Qaeda was not a hierarchical group after all but a dynamic network of cells and relationships. As I learned while doing research for my book “Top Secret America,” Flynn and McChrystal dramatically increased the pace of jsoc attacks on enemy hideouts by devising a system in which commandos on missions transferred promising data — cell-phone numbers, meeting locations — to analysts, who could then quickly point them to additional targets to hit. Multiple raids a night became common.

McChrystal, who was appointed to run jsoc in 2003, brought Flynn in as his intelligence chief to help him shake up the organization. Flynn was one of the few high-ranking officers who disdained the Army’s culture of conformity. But McChrystal also knew he had to protect Flynn from that same culture. He “boxed him in,” someone who had worked with both men told me last week, by encouraging Flynn to keep his outbursts in check and surrounding him with subordinates who would challenge the unsubstantiated theories he tended to indulge. [Continue reading…]