The CIA is running secret prisons around the world where they are sending prisoners for torture. These prisons are not new, the infrastructure for these prisons have been under construction since the 1970's. Secret CIA Prisons in Your Backyard is an interview of two journalists who have been researching the story. They have published Torture Taxi: On the Trail of the CIA's Rendition Flights to document the results of their research.
The CIA have set up shell corporations who own airplanes. The airplanes are flown under contract from the CIA shuttling people and equipment around the world in secret flights. However since these are civilian owned airplanes, they are required to file flight plans and leave other bits of paper trail. That paper trail is trackable by individuals.
Beginning in 2002 flight watchers began noticing this series of flights that would, for example, start at Andrews Air Force base, stop somewhere and end up in Afghanistan.
Speaking as an average American citizen I am not in support of our government torturing people, and violating normal legal procedures. Secret prisons are completely in violation of the habeas corpus legal precedent, where the government is required to show the body when they are holding someone. Holding people in secret is in violation of that legal precedent, which is a core value of American Justice. How dare our government leaders violate this.