Daniel Klaidman of The Daily Beast reports that the White House will soon take the power to launch lethal drone strikes away from the CIA and make the program the exclusive domain of the Defense Department. Because the military and intelligence services operate under a different set of rules, the move would consolidate all drone operations under a single command and a single set of procedure. It could also (potentially) add new layers of transparency and accountability to what has become one of the government's most controversial operations.
The shift may not change much in the real world of missile strikes and terrorist hunting, as drones will continue to be a major tool in the U.S. arsenal. However, it could signal a major shift in the legal and diplomatic basis for the program. For example, one of the most important distinctions between CIA operations and military ones is the difference between "covert" and "clandestine." The military can keep its "clandestine" activities classified or secret—like say a SEAL team raid to kill a wanted terrorist. But if Congress or a judge asks, they can't pretend they didn't happen. The CIA, on the other hand, is allowed to declare certain missions to be "covert." (Like say, sneaking American citizens out of a hostile country.) That means that, legally, they can deny that program even exists, shielding those responsible from accountability and hiding them from the public.
That extra layer of accountbility matters a lot when making life or death decisions. Currently, the CIA has the power to decide on its own if a terorist is going to be targeted, and in certain circumstances can carry out an attack without further authorization. The most notable exception is Pakistan, where the Armed Forces require presidential authorization to carry out a mission within its borders, but the CIA doesn't.
As far back as last fall it was reported that John Brennan, who was then the President's chief counterterrorism advisor, was already looking to consolidate drone operations under the umbrella of Pentagon, believing that the military was better suited to handle armed drone operations. He seemed to be growing more uncomfortable with the idea of the Central Intelligence Agency morphing from a spy outfit into a lethal fighting force, especially one that decides on its own who deserves the "lethal" part. Meanwhile, the Defense Department has much stricter requirements that must be met before carrying out a military operation in a foreign country, the White House and Congress have more power over generals (and their budgets) than they do secret agents, and international law and diplomacy helps to keep uniformed soliders on a tighter leash.
It's interesting to see that even though Brennan is now in charge of the CIA he hasn't changed his mind about dumping drones from his portfolio, and is legitimately committed to seeing the agency focus more on its spying roots. Giving the power to strike overseas solely to the president may not ease everyone's fears about the drone program, but at least it makes it slightly easier to keep an eye on it.