The FBI's transformation from a crime-fighting agency to a counterterrorism organization in the wake of the Sept. 11, 2001, attacks has been well documented. Less widely known has been the bureau's role in secret operations against al-Qaeda and its affiliates in Iraq and Afghanistan, among other locations around the world. With the war in Afghanistan ending, FBI officials have become more willing to discuss a little-known alliance between the bureau and the Joint Special Operations Command (JSOC) that allowed agents to participate in hundreds of raids in Iraq and Afghanistan. The relationship benefited both sides. JSOC used the FBI's expertise in exploiting digital media and other materials to locate insurgents and detect plots, including any against the United States. The bureau's agents, in turn, could preserve evidence and maintain a chain of custody should any suspect be transferred to the United States for trial. In early 2003, two senior FBI counterterrorism officials traveled to Afghanistan to meet with the Joint Special Operations Command's deputy commander at Bagram air base. The pace of activity in Afghanistan was slow at first. An FBI official said there was less than a handful of [Hostage and Rescue Team] deployments to Afghanistan in those early months; the units primarily worked with the SEALs as they hunted top al-Qaeda targets. The tempo quickened with the U.S.-led invasion of Iraq in 2003. At first, the HRT's mission was mainly to protect other FBI agents when they left the Green Zone, former FBI officials said. In 2005, all of the HRT members in Iraq began to work under JSOC.
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