Between the end of the Cold War and 9/11, the C.I.A. had declined in some areas while growing stronger in other areas. The areas of its strength did not match well with the immediate needs of counter-terrorism. The areas of its weakness were just those areas where competence was in high demand. Secretary of Defense Donald Rumsfeld knew very well the weaknesses of the C.I.A. because he had served on several task forces on intelligence during the previous Bush and Clinton administrations. It would take several years to bring the C.I.A. back to full strength. The terrorists were not going to wait in a neutral corner until the Americans got back on their feet and the referee allowed the fight to continue. If the C.I.A. could not fill the leadership role, then some other organization would have to lead.
Very soon, Secretary of Defense Donald Rumsfeld began to press for “the civilian leadership in the Pentagon, and not the C.I.A., [to get] the lead in fighting terrorism.” (p. 17.) What Rumsfeld wanted was “to get the U.S. Special Forces community into the business of what he called…”manhunts,”…” (p. 16.)
Immediately following 9/11, Rumsfeld ordered General Charles Holland, commander of Special Operations, to come up with a list of known terrorist targets for immediate attack. (p. 265.) In October 2001, numerous cases occurred where either Air Force pilots or Special Forces teams were prevented from striking at suspected Al Qaeda targets by various bureaucratic and/or legalistic restrictions. (pp. 48-49.) At about the same time, Holland provided a list, but warned that there was a dearth of “actionable intelligence” to support any rapid attack. (p. 266.) Rumsfeld suggested that Special Operations be made a “global command” directly under the command of the Secretary of Defense, with responsibility for all military operations against terrorists. (p. 271.)
In late 2001 or early 2002, President George W. Bush signed a legally required “finding” that authorized the Department of Defense to create a special unit to attack Al Qaeda. Henceforth, Hersh identifies this program as the SAP (for “special access program”). (p. 16.) This “highly secret program….was given blanket advance approval to kill or capture and, if possible, interrogate high-value targets…..The program would recruit operatives and acquire the necessary equipment, including aircraft, and would keep its activities under wraps.” (p. 49.) “In theory, the operation enabled the Bush Administration to respond immediately to time-sensitive intelligence: commandos crossed borders without visas and could interrogate terrorism suspects deemed too important to for transfer to the military’s facilities at Guantanamo. They carried out instant interrogations, often with the help of foreign intelligence services—using force if necessary—at secret C.I.A. detention centers scattered around the world.  The intelligence would be relayed to the SAP command center in the Pentagon in real time, and sifted for those pieces of information critical to the “white,” or overt world.” (p. 50.) In July 2002 Rumsfeld ordered General Holland, commander of Special Operations, “to develop a plan to find and deal with members of terrorist organizations…The objective is to capture terrorists for interrogations or, if necessary, to kill them, not simply to arrest them in a law-enforcement exercise.” (p. 265.)
The Defense Department was going to collect and analyze intelligence on terrorism.
 See: http://en.wikipedia.org/wiki/Special_access_program The Wikipedia entry illustrates some of Hersh’s problems. There are a host of “Special Access Programs.”