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WASHINGTON — Before leading chants of “Lock her up!” and endorsing the “extreme vetting” of Muslim immigrants, Lt. Gen. Michael T. Flynn, a retired career intelligence officer and registered Democrat who is advising Donald J. Trump, was already denouncing what he saw as the Obama administration’s failure to tackle Islamist militancy and the many faults of Hillary Clinton.

But if few people were listening before this year’s presidential campaign, many are now.

General Flynn, 57, took a star turn at the Republican convention in July, and no matter who wins in November, he appears likely to emerge from the campaign as the angry voice of what could best be described as the alternative right of the American national security establishment.

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For now, though, his focus is on getting Mr. Trump elected. General Flynn talks to his candidate multiple times a week, has sat in on the two intelligence briefings that the Republican nominee has received, and is part of the team that is helping to prepare Mr. Trump, as much as it can, for the third and final presidential debate on Wednesday, when national security is supposed to be one of the night’s six topics.

In an election year filled with strange and jarring turns, General Flynn’s entry into politics may be one of the most unusual. He has gone from being one of the most respected military officers of his generation to one of its most openly partisan, loudly inveighing against what he sees as a corrupt Washington elite that has left the United States weak and vulnerable.

No one else on Mr. Trump’s national security team comes with the pedigree of General Flynn, who was director of the Defense Intelligence Agency until 2014, and no one has brought the same level of vitriol.

“What’s happening with the U.S.? Where’s the leadership? That’s what I want to see change,” he said in an interview. “Am I angry or frustrated? Yeah. Who wouldn’t be?”

He is angry about the “political correctness” that makes President Obama and Mrs. Clinton shy from even uttering the phrase “radical Islamic terrorism” — a phrase the general makes a point of using, often — never mind tackling the very real threat he believes it poses. He is angry about what he sees as the lack of accountability represented by Mrs. Clinton and her emails. He is angry that the United States, under both Republicans and Democrats, keeps blundering into wars that seem only to make enemies of what should be natural allies, like Russia, in the fight against Islamist militancy.

It has left friends and critics alike wondering where General Flynn’s ideas end and Mr. Trump’s begin.

“I wasn’t surprised to hear him being outspoken when he retired,” David Hall, a retired Navy Reserve officer and federal prosecutor, said of General Flynn, with whom he worked in the Pentagon. “He was always willing to speak up when he was frustrated or the process wasn’t going well.”

“But going overtly political really surprised me,” Mr. Hall said. “I’d never heard him make any political remarks, or even a remark that I could view as a disguised political remark.”

General Flynn said he had become involved in the Trump campaign out of the same patriotic duty that led him to a 33-year career in the military. But for all the harsh talk, he can strike surprisingly bipartisan notes. He said, for example, that he would have advised Mrs. Clinton had she reached out to him.

“Whatever the outcome of this election, I would like to think that people would still say, ‘Look, this guy has some expertise,’” he said.

Unless Mr. Trump wins, that is unlikely to happen. General Flynn these days is as much of an outcast as one can be in the Washington national security establishment, much of which has lined up behind Mrs. Clinton.

That seems just fine with General Flynn. He has little patience for the Republican neoconservatives who led the United States into Iraq during the George W. Bush administration — “they’ve gotten us into mess after mess for the wrong reasons” — and he sees the Democratic national security establishment as no better.

“Hillary Clinton pushed to get us into Libya. Is she a neocon on the Democratic side?” he said. “We’re in too many conflicts that just seem to be perpetual.”

He is also not uncritical of the Republican nominee. He called the recording of Mr. Trump talking about grabbing and kissing women “disgusting,” and he said he and others had advised Mr. Trump to take a tougher line with Russia before the previous debates, especially when it came to the hacking of the Democratic National Committee and Clinton campaign staff members.

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The United States should be cultivating Russia as an ally to fight Islamist militancy, he said, but “do I want Russia to influence our election? Absolutely not.” He added, “They need to be told in no uncertain terms to knock it off.”

But General Flynn is dismissive of former colleagues in the military who have privately and publicly urged him to dial back his support for Mr. Trump.

“They’re saying, ‘You’re using your title in politics.’ So? You’re not using your titles, admirals and generals, to get on corporate boards?” General Flynn said.

“I care deeply about this country,” he continued. “I actually found it very disrespectful that those guys would come out and counsel me publicly.”

In any case, General Flynn never saw himself as part of their club. He did not come to the military with the West Point pedigree of many of his peers — he graduated from the Army’s Reserve Officers Training Corps program at the University of Rhode Island — and his roots were scrappier than those of most generals, he said, describing his family as “definitely lower middle class.”

During his time in the Army, General Flynn earned a reputation for being outspoken and unconventional and, in the years after the Sept. 11 attacks, for being unusually good at taking apart terrorist networks. He helped reshape the Joint Special Operations Command at the height of the war in Iraq, ran military intelligence in Afghanistan during the Obama administration’s troop surge and was named director of the Defense Intelligence Agency by Mr. Obama in 2012.

But his term at the agency was cut short after two years. His detractors say that he lacked the experience to manage an operation with 20,000 employees, and that his efforts to overhaul what he saw as an ineffective bureaucracy left the agency a chaotic mess. His proponents say he was done in by an old guard that was being sidelined.

General Flynn maintains that he was fired for insisting that Al Qaeda and other militant Islamists were regrouping in the Middle East and for refusing to fall in line with an administration that wanted to bask in the glow of having killed Osama bin Laden. His view of the threat posed by Islamist militancy has hardened in the two years since he was forced into retirement.

Yet General Flynn also talks of the need to strengthen relationships with predominantly Muslim countries and to better understand their cultures. Muslim countries are eager to play a bigger role in the fight against Islamist militancy, he said. What they are lacking is American leadership, he said, and Mr. Trump can provide it.

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