'By early 2002, the CIA, the Justice Department, and the National Security Council were debating whether the legal and humanitarian protections of the Geneva Conventions would apply to captives suspected to be members of al-Qaida or the Taliban. After weeks of debate, and over objections from the State Department, President George W. Bush ultimately issued the final word on the matter. In a February 2002 memo, he stated that al-Qaida and Taliban detainees were not protected by the Geneva Conventions.'
This is one of the roots of the problem. Once you have a class of people without rights, you can arbitrarily identify people as part of that class and they have no chance at due process. Unless absolutely everyone has basic legal protections, no one has them.