In 2010, then-Maj. Gen. Michael Flynn, at the time the top U.S. military intelligence official in Afghanistan, slammed the U.S. spy apparatus he helped to oversee as bloated and out of touch. Four years later, he was fired as the head of the military’s largest intelligence agency—in his view for speaking truth to power about the inadequacies of the nation’s national security preparedness.

Today, Gen. Flynn, who retired in 2014 as a lieutenant general, is in a position to again push his views of how America should protect itself,...