JIM SCIUTTO: That's right. General Flynn, he had distinguished command roles in both Iraq and Afghanistan but he has also spread conspiracy theories. He allegedly mishandled classified information, and he was fired from his last military post, but he will soon serve as President-elect Trump's closest national security adviser. Now activist groups are pressing Mr. Trump to cut ties.

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He's tapped to be President-Elect Trump's closest adviser on the most sensitive threats facing the nation. And tonight there is growing criticism that his inflammatory views make him unfit for the job. More than 50 progressive nonprofits, ranging from religious to social justice organizations, signed a letter asking Trump to dump Flynn.

MICHAEL FLYNN: Islam is a political ideology. It is a political ideology. It definitely hides behind this notion of it being a religion.

SCIUTTO: Citing the former Defense Intelligence chief's numerous Islamophobic remarks, including tweeting in February that “fear of Muslims is rational.” Today, Vice President-elect Mike Pence praised Flynn on CNN.

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But the groups also raised more substantive allegations. On one occasion, while overseeing intelligence in Afghanistan, former government officials tell CNN that Flynn shared classified information from another agency with Pakistan. Flynn told CNN the allegation, quote, “is not true. Not even close.” But the incident led to an informal reprimand, though no charges, officials tell CNN. And even as Flynn received classified intelligence briefings during the campaign, he was lobbying on behalf of foreign clients. Among them, Turkey, who Flynn has uncritically backed as it has cracked down on domestic dissent. Trump's transition team told CNN last month that Flynn's dealings with Turkey were within his rights as a private citizen and that Flynn would sever ties to his consulting firm when he is part of the administration.

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In his public statements, Flynn has repeatedly dabbled in conspiracy theories. Just one week before the election, he tweeted, quote, “you decide. NYPD blows whistle on new Hillary e-mails. Money laundering, sex crimes with children, et cetera. Must read.” Allegations that remain entirely unsubstantiated.

Flynn's son, Michael Flynn, Jr., who served as his aide, has been a leading proponent of a bizarre fake news story alleging that a D.C. pizzeria was home to a child sex ring, visited by Clinton campaign staff. The story led an armed man to enter the restaurant this weekend, he claimed, to investigate the allegations. He was arrested only after firing several shots. And yet on Sunday, Flynn, Jr. was still defending the conspiracy theory, tweeting, quote, “until Pizzagate, proven to be false, it will remain a story. The left seems to forget Podesta emails and the many coincidences tied to it.” Today Flynn, Jr. was dismissed from the transition. The decision, sources tell CNN, coming directly from the president-elect.