In 1996 the Defense Intelligence Agency and US Special Operations Command, under Joint Chiefs of Staff General Hugh Shelton and General Peter Schoomaker (Special Operations Command), constructed a covert signals intelligence program, code named, Able Danger. This unit would involve members of the Land Information Warfare Activities division with some of the most highly skilled tech analysts in the country. One of the members of this program, Major Anthony Shaffer, was already a highly decorated Army counter-intelligence officer, and was selected to the Able Danger unit. The operation involved data-mining which would later uncover two of three al-Qaeda active cells. The 'Brooklyn cell' linked to "Blind Sheik" Omar Abdel-Rahman, the other headed by Mohamed Atta along with three others linked to the 9/11 attacks.
However the program ran into resistance from SOCOM lawyers and Department of defense officials who determined that Atta and the cell were US persons and ordered that most of the Able Danger data destroyed. In 2003, while in Afghanistan fighting against the Taliban, Shaffer would give an interview to 9/11 Commission Director Phillip Zelikow, detailing the Able Danger program and what it compiled. When Shaffer returned to the United States he was shocked to learn that the Department of Defense had suspended his security clearance and levied "false allegations" against him. The Army Trial Defense Services heard his case and cleared him of the charges against him. Shaffer's story is told in full here in todays episode.
Operation Dark Heart: Spycraft and Special Ops on the Frontlines of Afghanistan -- and The Path to Victory:
London Center for Policy Research: