Mr. Muhammad and his followers had been killed by theC.I.A., the first time it had deployed a Predator drone in Pakistan to carry out a “targeted killing.” The target was not a top operative of Al Qaeda, but a Pakistani ally of theTaliban who led a tribal rebellion and was marked by Pakistan as an enemy of the state. In a secret deal, the C.I.A. had agreed to kill him in exchange for access to airspace it had long sought so it could use drones to hunt down its own enemies.

That back-room bargain, described in detail for the first time in interviews with more than a dozen officials in Pakistan and the United States, is critical to understanding the origins of a covert drone war that began under the Bush administration, was embraced and expanded by President Obama, and is now the subject of fierce debate. The deal, a month after a blistering internal report about abuses in the C.I.A.’s network of secret prisons, paved the way for the C.I.A. to change its focus from capturing terrorists to killing them, and helped transform an agency that began as a cold war espionage service into a paramilitary organization.

The C.I.A. has since conducted hundreds of drone strikes in Pakistan that have killed thousands of people, Pakistanis and Arabs, militants and civilians alike. While it was not the first country where the United States used drones, it became the laboratory for the targeted killing operations that have come to define a new American way of fighting, blurring the line between soldiers and spies and short-circuiting the normal mechanisms by which the United States as a nation goes to war.

These are military operations, right? Why is the CIA allowed to perform military operations?

they have paramilitary operations...the line has always been blurry for special operations/intelligence 

Just as long as the commander-in-chief is really calling the action I guess that's okay.

But man does the president have a lot of power now.