The fact that both the military and the CIA have carried out UAV operations created problems of role definition that are almost the opposite of those in the counterinsurgency situation. There, reconstruction functions had traditionally been considered civilian, but persistent violence, shortages of civilian personnel and resources made it difficult to avoid military participation. In the case of targeted killing, the function seems more clearly a military one, but is also carried out by civilians in the CIA. While it is true that parts of the CIA have had a covert, quasi-military role since the passage of the National Security Act of 1947, routine conduct of bombing operations, even remotely, seems closer to a traditional military function.

The reasons for public discomfort about widespread use of UAVs to strike terrorists are complex. Apart from legal issues, some of this concern amounts to more than just a feeling that it is more appropriate for the military to be responsible for conducting violence than the civilian CIA. Discomfort seems also to revolve around the institutional reputation of the CIA – its secrecy and history of acts of questionable legality. First, although the CIA has long been involved in covert operations, its reputation has been increasingly tarnished since 9/11, even as it recovered somewhat from the Bay of Pigs disaster more than a half century ago, and even from the Church Committee findings in the 1970s. Widespread abuses of enhanced interrogations, practices such as waterboarding, extraordinary renditions of suspects, maintenance of secret “black” sites, and even indications that CIA leadership has hidden some agency activities from high government officials have all heightened internal and international public impressions of the agency's rogue behavior.

Second, lack of public discourse about the legality of targeted killing has further heightened impressions of a lack of accountability. This is discussed in Chapter 8.