Soon after the September 11 attacks in 2001, the United States captured hundreds of suspected al-Qaeda terrorists in Afghanistan and around the world. By the following January the first of these prisoners arrived at the U.S. military’s prison camp in Guantanamo Bay, Cuba, where they were subject to President George W. Bush’s executive order authorizing their trial by military commissions. Jess Bravin, the Wall Street Journal’s Supreme Court correspondent, was there within days of the prison’s opening, and has continued ever since to cover the U.S. effort to create a parallel justice system for enemy aliens. A maze of legal, political, and moral issues has stood in the way of justice—issues often raise...