Ever Wonder Why “The Left” Went After General Flynn?

WASHINGTON — Long before Lt. Gen. Michael T. Flynn became Donald J. Trump’s choice for national security adviser, he believed that the Central Intelligence Agency had become a political tool of the Obama administration — a view now echoed by the president-elect in his mocking dismissals of C.I.A. assessments that Russia sought to tip the election in Mr. Trump’s favor.

“They’ve lost sight of who they actually work for,” Mr. Flynn said in an interview with The New York Times in October 2015. “They work for the American people. They don’t work for the president of the United States.” He added, speaking of the agency’s leadership: “Frankly, it’s become a very political organization.”

Mr. Flynn’s assessment that the C.I.A. is a political arm of the Obama administration is not widely shared by Republicans or Democrats in Washington. But it has appeared to have been internalized by the one person who matters most right now: Mr. Trump.

In the past few days, Mr. Trump has sought to portray reports of the agency’s assessments that Russia actively tried to interfere in the election as a desperate attempt by sore losers to taint his presidency before it begins. His denigration of C.I.A. officials as “the same people that said Saddam Hussein had weapons of mass destruction” has opened up an extraordinary rift between the president-elect and the nation’s intelligence community that is unlikely to be bridged anytime soon.

Mr. Flynn also appears to have helped set the tone for Mr. Trump’s testy relationship with the intelligence community. In August, when the Trump campaign received its first intelligence briefing, Mr. Flynn was so combative with the briefers that another person in the room had to urge him to settle down, according to a person familiar with the episode who was told about it in confidence.

On any number of issues — from the Obama administration’s failure to foresee the rise of the Islamic State to Mr. Flynn’s ouster as chief of the Defense Intelligence Agency, the intelligence arm of the Defense Department — he has made it clear in recent years that he sees the political hand of the C.I.A. at work.

As director of the D.I.A. from 2012 to 2014, he pushed hard for his agency, long treated as second-rate by the C.I.A., to be given greater access to the trove of documents and other materials seized during the raid that killed Osama bin Laden in Abbottabad, Pakistan, in May 2011. The C.I.A. controlled the material, and Mr. Flynn became convinced that the agency was refusing to share or declassify much of it because of fears that it would undermine the administration’s narrative about Al Qaeda’s waning strength at the time Bin Laden was killed.

“It’s all political with” the C.I.A. leadership, Mr. Flynn said in the 2015 interview, which focused on the rise of the Islamic State and American national security.

“If they put out what we knew, then the president could have not said, in a national election, ‘Al Qaeda’s on the run and we’ve killed Bin Laden,’” he said, referring to Mr. Obama’s 2012 re-election campaign. “Even today, he talks about Bin Laden as though that was a stroke of genius.”

Mr. Flynn also questioned the decision to kill Bin Laden. “Killing Bin Laden was the wrong thing to do,” he said. “They could have captured him.”

In killing Bin Laden, he said, “we created a new version of Allah.”

“What we should have done is shown him to be a decrepit old guy, put him in a freaking cage, in a cell, and put him on trial,” Mr. Flynn added. “Make it a big messy trial, make it global.”

Mr. Flynn has also said that the C.I.A., at the urging of the White House, was playing down warnings from the D.I.A. about the resurgence of Al Qaeda in Iraq, which would later become the Islamic State. “I’m telling you, the C.I.A. has a lot to reflect on because of this,” he said.

A number of current and former officials dispute Mr. Flynn’s account, saying concerns about the resurgence of Islamist militants in the midst of Syria’s civil war were widespread in the intelligence community.

Mr. Flynn, who was fired from the D.I.A. after serving only two years of a three-year appointment, has described his dismissal as an act of political retribution by the C.I.A. and Obama administration officials who did not want to hear what he was saying.

Other officials, including some with direct knowledge of the decision to dismiss Mr. Flynn, said he was forced out for a more straightforward reason: He was not a good manager, and his efforts to reform the agency left it in chaos.

It was not Mr. Flynn’s first run-in with the civilian intelligence community. The ill will stretches back years, current and former officials said, and it transformed into open hostility when Mr. Flynn was running military intelligence under Gen. Stanley A. McChrystal in Afghanistan.

In January 2010, after less than a year on the job, Mr. Flynn released a paper, “Fixing Intel,” that was highly critical of American intelligence work in Afghanistan. It bluntly stated that “the U.S. intelligence community is only marginally relevant to the overall strategy,” and said that it had only itself to blame because it had failed to understand Afghanistan’s cultural complexities.

The paper was widely praised in defense circles as insightful. But at the C.I.A., officials were furious at what they saw as a direct attack on the aptitude and professionalism of the roughly 1,000 agency personnel who were serving in Afghanistan at the time.

They were also incensed at the timing of the paper, which became public five days after a suicide attack that killed seven C.I.A. officers at a base in eastern Afghanistan. Mr. Flynn’s searing critique was seen at the agency as the height of insensitivity.

Mr. Flynn has been unapologetic about his views of not only the C.I.A. but other national security agencies, including the D.I.A. under his leadership.

“They’ve really been lying to the American public,” he said in the interview, referring to the Obama administration and much of the national security and intelligence establishment. “The Department of Defense and those of us that have allowed this sort of a happy talk — ‘We’re moving in the right direction, things are working.’ It’s not. The Taliban are going to come back into power, or ISIS is going to come back into power.”