"The war that is going on between the CIA and the bad guys in this part of the world is a real war," says Tim Weiner, author of "Legacy of Ashes: The History of the CIA." "The CIA is targeting them with missiles fired by drone aircraft and they are taking their revenge in the way they know best -- which is to kill the people who are trying to kill them. ... This attack is one of the consequences of using targeted killing as a weapon of war."
The drone program relies on informants who can cross the border easily, in parts CIA officers cannot. The CIA is wary of making major trips into Pakistan for fear of the repercussions if officers were caught or killed there. Informants -- especially Pakistani informants from the Waziri or Mehsud tribe -- are the most valuable assets for the CIA in finding senior al Qaeda and Taliban militants who are targeted by the drone program.
"To go after the Taliban and the Haqqani network on the Pakistani side of the border, the United States relies almost exclusively on its predator drones. But those predator drones require agents on the ground to direct them, to say, 'this is where you should be looking,'" says Richard Clarke, the Bush administration's counter-terrorism czar until 2003 and an ABC News consultant. "The CIA does that in support of the military, and without their intelligence, we really have very little way of affecting what's going on on the Pakistani side of the border."
The most likely Taliban group to have perpetrated the attack is the one led by Sirajuddin Haqqani, the son of Jalaluddin Haqqani, one of the CIA's most important assets when the agency was helping fund the Afghan mujahedeen fighting the Soviets in Afghanistan. The Haqqanis have been running militant operations for 30 years and have recently become perhaps the most lethal commanders targeting U.S. troops in Afghanistan. They are based in North Waziristan but control large parts of Khost and other provinces in eastern Afghanistan as well.
The Haqqanis have also kidnapped the only known American soldier in enemy custody -- PFC Bowe Bergdahl -- according to a senior NATO official. Since Bergdahl was kidnapped in late June, the official says the Haqqanis "have been getting pounded" and a "great many of their mid to senior leaders have been captured and/or killed."
The infiltration into the CIA base suggests an extremely high level of sophistication, even for a network that has a huge reach across the area.
"The Soviet Union during the Cold War, the Cubans during the Cold War were able to run double agents against the CIA very successfully," says Clarke. "But for a non-nation state to be able to do this -- for the Haqqani network of the Taliban to be able to do this -- represents a huge increase in the sophistication of the enemy."
Clarke and other former intelligence officials predict the CIA in Afghanistan will be forced to question who they can trust and change their methods in how they find informants.
"Because of this attack, the CIA will be very, very careful about who it trusts, how it vets its agents, how it searches its agents," Clarke says. "And this will mean that in the future, it will be much more difficult for CIA to operate in the field because of probably new security roles affecting what they do."