By Samuel Burke & Ken Olshansky, CNN

The story of how America's Central Intelligence Agency got back into the killing business after September 11th has, for the most part, been kept under wraps.

The secret weapons, targets and killings have had little-to-no oversight by the U.S. Congress, the courts or the press.

Now, New York Times correspondent Mark Mazzetti has uncovered key moments of America's shadow war. In his new book, "The Way of the Knife," the Pulitzer Prize-winning author reports on how the CIA morphed from an intelligence agency to a paramilitary force, and the complicated route to get it back again.

In an interview with CNN’s Christiane Amanpour on Wednesday, Mazzetti said the name of the book came from analogy originally used by John Brennan – now the CIA director – formerly President Obama's top counterterrorism adviser.

Brennan gave a speech in which he compared some CIA practices to using a “scalpel,” implying a clean surgery without complications. However, Mazzetti’s book examines the very complicated risks and ramifications of this kind of warfare.

President Bush authorized drone strikes, but his use of them was minimal – at least compared to Obama’s. There were 37 targeted airstrikes in 2008, compared to 121 in 2010, according the Long War Journal.

It all began in 2004, when the CIA was trying hard to get armed drones into Pakistan. The U.S. managed to kill a militant named Nek Muhammad, using a drone in June of that year, according to Mazzetti. Despite being affiliated with al Qaeda, Mazetti reports that Muhammad was actually more of Pakistan's problem than the United States’.

“There was a deal that was cut between America and the Pakistani spies to kill Nek Muhammad,” Mazzetti told Amanpour, paving the way for these types of killings to commence.

It took a few years for the program to ramp up, but it was not until the end of the Bush administration in 2008 that the strikes really escalated.

Then President Obama took office, embraced the strikes and expanded the program even further.

“As we found in Pakistan and also in Yemen, the groups that get hit are not just al Qaeda senior leaders,” Mazzetti said. “And to be honest, in Pakistan, there are very few of the original al Qaeda leadership as it existed on 9/11.”

According to Mazzetti, the CIA is also targeting members of the Haqqani network and the Pakistani Taliban – so while Pakistan says it is against the drone program, the government is willing to bless some strikes because the U.S. is hitting enemies of Pakistan.

Now, Brennan has hinted he might move the program to the Pentagon, allowing the CIA to revert back to being an intel-gathering spy machine – though that transfer might be easier said than done.

Can the United States government use a drone to kill an American citizen sitting in a cafe who doesn't pose an immediate threat? That’s precisely what U.S. Senator Rand Paul, a Republican of Kentucky, recently asked the United States government. The U.S. Attorney General answered the question, declaring any such action unlawful.

But the U.S. Justice Department did develop a legal analysis that cleared the path for the U.S. to use a drone to kill U.S.-born Anwar al-Awlaki, accused of plotting the so-called underwear bombing of a plane in 2009.

The Obama administration won't be able to keep the secretive, targeted assassination drone program, as closely under wraps any more. It's erupted into a full public airing over Obama's new CIA chief, John Brennan. In the video above, CNN’s Christiane Amanpour speaks with Pulitzer prize winning New York Times reporter Charles Savage, who has uncovered many of the details of the U.S. drone program.

When can America kill Americans?

PART 1: CNN's Christiane Amanpour explores how U.S. drones have been used to kill Americans.

When can America kill Americans?

PART 2: CNN's Christiane Amanpour explores how U.S. drones have been used to kill Americans.

By Samuel Burke & Ken Olshansky, CNN

For much of the world, drones represent everything that is wrong with American foreign policy. The sizable majority of Americans, on the other hand, have no problem with them.

In the latest polling, 75% of Americans approve of the use of unmanned aircrafts against terrorist suspects overseas.

In the countries that are on the receiving end of drone attacks, such as Pakistan and Yemen, there is rage. As well as significant evidence that drones have killed and injured civilians.

In Washington on Thursday, the secretive policy had its first official public airing, as Congress started confirmation hearings for John Brennan, whom President Obama has nominated by to be the next CIA director. Brennan is currently President Obama’s counterterrorism chief and the principle architect of the U.S. drone policy.

It was Brennan who first publicly admitted the existence of the drone program last year.

In a speech last year at the Woodrow Wilson Center, Brennan said, “Let me say it as simply as I can: Yes, in full accordance with the law and in order to prevent terrorist attacks on the united states and to save American lives the united states government conducts targeted strikes against specific al-Qaeda terrorists, sometimes using remotely piloted aircraft, often referred to publicly as drones. And i m here today because president Obama has instructed us to be more open with the American people about these efforts.”

Much remains secret about the drone program. Most notably is the “Kill List” – targets, including American citizens, that the President is said to personally approve.

Indeed, three Americans are known to have been killed by drones, including a 16-year-old American boy who was born in Colorado, who the son of American-born al Qaeda leader Anwar al-Awlaki.

The Brennan hearings may be an accountability moment.

Leading the charge is a Democratic Senator Ron Wyden, who has laid out some fundamental questions about the drone program.

“Every American has the right to know when their government believes it's allowed to kill them,” Senator Wyden said on MSNBC Thursday morning. “I don't think that, as one person said, that is too much to ask. And this idea that security and liberty are mutually exclusive, that you can have only one or the other, is something i reject.”

In the video above, CNN’s Christiane Amanpour puts Senator Wyden's questions to two experts: Mark Lowenthal, a former CIA official who approves of the U.S. drone policy; and Vince Warren, executive director of the Center for Constitutional Rights. Warren is one of the lawyers representing the al-Awlaki family’s case against the U.S. government.

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