That’s the charge the National Journal’s Marc Ambinder makes in his very interesting new book on Joint Special Operations Command, coauthored with D.B. Grady.

They write:

The U.S. intelligence community took advantage of the chaos to spread resources of its own into the country. Using valid U.S. passports and posing as construction and aid workers, dozens of Central Intelligence Agency (CIA) operatives and contractors flooded in without the requisite background checks from the country’s Inter-Services Intelligence (ISI) agency. Al-Qaeda had reconstituted itself in the country’s tribal areas, largely because of the ISI’s benign neglect. In Afghanistan, the ISI was actively undermining the U.S.-backed government of Hamid Karzai, training and recuiting for the Taliban, which it viewed as the more reliable partner. The political system was in chaos. The Pakistani army was focused on the threat from India and had redeployed away from the Afghanistan border region, the Durand line, making it porous once again. To some extent, the Bush administration had been focused on Iraq for the previous two years, content with the ISI’s cooperation in capturing senior al-Qaeda leaders, while ignoring its support of other groups tha would later become recruiting grounds for al-Qaeda.

A JSOC intelligence team slipped in alongside the CIA. The team had several goals. One was prosaic: team members were to develop rings of informants to gather targeting information about al-Qaeda terrorists. Other goals were extremely sensitive: JSOC needed better intelligence about how Pakistan tranported its nuclear weapons and wanted to pentrate the ISI. Under a secret program code-named SCREEN HUNTER, JSOC, augmented by the Defense Intelligence Agency (DIA) and contract personnel, was authorized to shadow and identify members of the ISI suspected of being sympathetic to al-Qaeda. It is not clear whether JSOC units used lethal force against these ISI officers; one official said that the goal of the program was to track terrorists through the ISI by using disinformation and psychological warfare. (The program, by then known under a different name, was curtailed by the Obama administration when Pakistan’s anxiety about a covert U.S. presence inside the country was most intense.)

Meanwhile, rotating teams of SEALs from DEVGRU Black squadron, aided by Rangers and other special operations forces, established a parallel terroris-hunting capability called VIGILANT HARVEST. They operated in the border areas of Pakistan deemed off limits to Americans, and they targeted courier networks, trainers, and facilitators. (Legally, these units would operate under the authority of the CIA any time they crossed the border.) Some of their missions were coordinated with Pakistan; others were not. As of 2006, teams of Green Berets were regularly crossing the border. Missions involved as few as three or four operators quietly trekking across the line, their movements monitored by U.S. satellites and drones locked onto the cell phones of these soldiers. (The cell phones were encrypted in such a  way that made them undetectable to Pakistani intelligence.) Twice in 2008, Pakistani officials caught wind of these missions, and in one instance, Pakistani soldiers operating in the Federally Administered Tribal Areas fired guns into the air to prevent the approach of drones.

Forward intelligence cells in Pakistan are staffed by JSOC-contracted security personnel from obscure firms with insider names such as Triple Canopy and various offshoots of Blackwater, but it is not clear whether, as Jeremy Scahill of the Nation has argued, the scale of these operations was operationally significant or that the contractors acted as hired guns for the U.S. government. Sources say that only U.S. soldiers performed “kinetic” operations; Scahill’s sources suggest otherwise. The security compartments were so small for these operations (one was known as QUIET STORM, a particularly specialized mission targeting the Pakistani Taliban in 2008) that the Command will probably be insulated from retrospective oversight about its activities. A senior Obama administration official said that by the middle of 2011, after tensions between the United States and the Pakistani government had reached an unhealthy degree of danger, all JSOC personnel except for its declared military trainers were ferreted out of the country. (They were easy to find using that same secret cell phone pinging technology.) Those who remained were called Omegas, a term denoting their temporary designation as members of the reserve force. They then joined any one of a dozen small contracting companies set up by the CIA, which turned these JSOC soldiers into civilians, for the purposes of deniability.

Source: Foreign Policy Blog