On a Saturday in January 2003, as the Iraq War approached, the Pentagon's Office of Net Assessment convened a meeting in a nondescript building in Arlington, Virginia, with three dozen of Washington's top conservative policy intellectuals. Using an information-gathering technique dating back to the Eisenhower administration, the office asked four groups to study the long-term threat the United States faced from international terrorism and to report back to Deputy Secretary of Defense Paul Wolfowitz.

One of the groups was led by Francis Fukuyama, a professor at Johns Hopkins' School of Advanced International Studies (SAIS), best known as the author of The End of History and the Last Man, the international bestseller that led British political philosopher John Gray to dub Fukuyama “[the] court philosopher of global capitalism.” The relationship between Fukuyama and Wolfowitz went back 35 years, to when Fukuyama was a Cornell undergraduate and Wolfowitz, then a Yale political-science professor, was a board member of the Telluride Association, the elite group house where Fukuyama lived. Fukuyama interned for Wolfowitz while a graduate student in the mid-1970s at the U.S. Arms Control and Disarmament Agency, and later followed his mentor to the State Department during the first Reagan administration. When Wolfowitz became dean of the SAIS, he recruited Fukuyama from George Mason.

When Fukuyama received the Pentagon's call, he immersed himself in subjects -- the politics of the Middle East, Islam, terrorism -- he hadn't thought about since he'd worked with Dennis Ross on the Palestinian autonomy talks that followed the Camp David accords...