In Afghanistan, the ISI was actively undermining the U.S.-backed government of President Hamid Karzai, training and recruiting 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 that would later become recruiting grounds for al-Qaeda.
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.
A senior Obama administration official said that by the middle of 2011, after tensions between the U.S. and the Pakistani government became particularly and perhaps dangerously high, 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.