The fall of Col. Muammar el-Qaddafi seemed to vindicate Hillary Clinton. Then militias refused to disarm,neighbors fanned a civil war, and the Islamic State found refuge. While the C.I.A. moved quickly to secure Colonel Qaddafi’s chemical weapons, other efforts fell short. ”“There was one arsenal that we thought had 20,000 shoulder-fired, surface-to-air missiles, SA-7s, that basically just disappeared into the maw of the Middle East and North Africa,” recalled Robert M. Gates, the American defense secretary at the time.” ”As she exited the State Department in February 2013, factional violence, which would break into open civil war in 2014, was...