As President Obama nominates John Brennan to lead the CIA, the future of the controversial program they've worked so closely on — America's targeted killing of terrorism suspects — swings into uncertainty: Will Brennan's restrictions on drone targets win out? Will he pull back on his push to give the CIA less power in the program? And will his confirmation hearings reveal key new details about a secret war?

Brennan's current official title is Deputy National Security Advisor and Assistant to the President for Homeland Security and Counterterrorism , making him Obama's closest confidant when it comes to intelligence and security matters. As such, one of his most prominent roles was overseeing the U.S.'s drone assassination programs in the Middle East and Africa, an ever-expanding practice of using unmanned aerial vehicles to hunt down and kill the world's terrorist leaders. Brennan is the face of the program, defending it in public — his speech last year was one of only two detailed accounts by senior administration officials — as he has been put in charge of efforts to make the program more transparent at the same time that he makes it more effective. That also means making it less dangerous, by restricting targets to only the most senior terrorist leaders and reducing civilian casualties and other collateral damage. However, America's "Assassination Czar" will forever be the man most associated with the controversial practice. Which may or may not be a bad thing: "If John Brennan is the last guy in the room with the president, I'm comfortable, because Brennan is a person of genuine moral rectitude," drone critic and Yale law-school dean Harold Koh told The New York Times in its investigation of the program.

But as soon as David Petraeus vacated the CIA director's chair last November, critics were already arguing that Brennan should not be allowed to take over, precisely because of the troubling nature of his drone-first counter-insurgent strategy. Brennan has often stated that the program doesn't spread anti-American sentiment in Yemen and Pakistan, but few people seem to buy that line of argument, believing at the very least that the citizens of other nations resent when foreigners launch missiles at them without warning. 

However, even before that, Conor Friedersdorf over at TheAlantic.com made a compelling argument that there was one man working to rein in the CIA excesses and bring the drone program under tighter control: John Brennan.

The truth is that the U.S. drone war is actually two different, but related programs — the military's and the CIA's — each with conflicting jurisdictions, rules, and procedures. Because Afghanistan is an active war zone, the Pentagon is free to conduct drone operations in that country as it sees fit, striking whenever it deems necessary. In places like Yemen or Somalia, the Navy or Air Force may take part on a case-by-case basis, but all military (or CIA) operations must be directly approved by the President. Pakistan, however, is a different story. The Pakistani government refuses to allow the U.S. military to operate within its borders, yet the Taliban and other terrorists run rampant in the more lawless parts of the country. That's where the CIA comes in. 

According to reporting from The Washington Post, in any other country, the CIA needs explicit White House permission to carry out a drone strike, but in Pakistan they were given free reign to target anyone on a pre-approved "kill list," without checking with Brennan or the President first. Once someone was on the list, that was it for them. And the spies at the CIA were increasingly eager to add new names to that list.

All indications were that Brennan wanted take that power away from the CIA and consolidate the drone program as a purely military operation. Putting the actual job of flying drones and launching missile strikes into the hands of the better-equipped and better-trained Pentagon would give the program more transparency and bring the actual "kill list" under tighter control: Brennan's control. The political realities in Pakistan made it difficult to cut the CIA out entirely, but there was still a chance to ensure that the White House would have more direct control over their operations. The implication, according to Friedersdorf, was that even the man who made drone war such a vital part of America's counterterrorism effort was worried that it was already too big to contain.

But now that Brennan wants to move out of the White House and into the CIA, will he want to bring the control of the drone program with him, putting it back into the hands of spies, and not soldiers? Brennan pushed back against the CIA while working with the president, despite 25 years of service in the intelligence community. He spent the last few years of his career trying to bring the secret drone war out of the shadows of the clandestine spy services, by consolidating its power under his office. Is he now going to walk away from that office and hand that power to someone else? Will he argue for more CIA control, now that he's in control of the CIA? Or will he use his new position to further ensure that the program is protected from himself and his successors?

As an appointee who never needed Senate approval, Brennan hasn't had to answer questions like these before, and it remains to be seen if any lawmakers will ask him before approving his nomination. In 2009, it was Democrats on the left who scuttled Brennan's nomination to the same CIA post, because he was too closely associated with the CIA torture program promoted under the previous president. Now, he's solidified another policy that began under President Bush and is ready to head back to the CIA as its biggest booster. Whether or not the drone program continues as an intelligence effort or a military one, Brennan has ensured that, for better or worse, it will always be a key part of America's fighting overseas.