The National Security Advisor is a president's main foreign policy person and plays a key role as coordinator of implementing thepresident's foreign policy decisions. Bearing that in mind, Gen. Flynn, seen as one of Trump's closest and most trusted advisors, takes the view that the U.S. is in a global war, not just against Islamic jihadists but against Islam itself. It's not really a religion, Flynn argues, but a dangerous political ideology. Flynn has called Islam a "cancer" and has said, "Fear of Muslims is rational." In April 2015 he told Fox News, "I've been at war with Islam, or a component of Islam, for the last decade."

According to Dana Priest in the New Yorker, "The greatest accomplishment of Flynn's military career was revolutionizing the way that the clandestine arm of the military, the Joint Special Operations Command, undertook the killing and capture of suspected terrorists and insurgents in war zones."