The decision reflected both Obama's belief in the need to move aggressively in Pakistan and the influence of the CIA in the new administration. To a far greater extent than the Bush White House, Obama and his top aides relied on the CIA for its analysis of Pakistan, according to current and former senior administration officials. As a result, preserving the agency's ability to carry out counterterrorism, or "CT," operations in Pakistan became of paramount importance.

"The most important thing when it came to Pakistan was to be able to carry out drone strikes and nothing else," said a former official who spoke on condition of anonymity. "The so-called strategic focus of the bilateral relationship was there solely to serve the CT approach."

Initially, the CIA was right. Increased drone strikes in the tribal areas eliminated senior al Qaeda operatives in 2009. Then, in July 2010, Pakistanis working for the CIA pulled up behind a white Suzuki navigating the bustling streets of Peshawar. The car's driver was later tracked to a large compound in the city of Abbottabad. On May 2, 2011, U.S. commandos killed Osama bin Laden there.

The U.S. intelligence presence, though, extended far beyond the hunt for bin Laden, according to former administration officials. At one point, the CIA tried to deploy hundreds of operatives across Pakistan but backed off after suspicious Pakistani officials declined to issue them visas. At the same time, the agency aggressively used the freer hand Obama had given it to launch more drone strikes than ever before.

Established by the Bush administration and Musharraf in 2004, the covert CIA drone program initially carried out only "personality" strikes against a preapproved list of senior al Qaeda members. Pakistani officials were notified before many, but not all, attacks. Between 2004 and 2007, nine such attacks were carried out in Pakistan, according to the New America Foundation.

In 2008, the Bush administration authorized less-restrictive "signature" strikes in the tribal areas. Instead of basing attacks on intelligence regarding a specific person, CIA drone operators could carry out strikes based on the behavior of people on the ground. Operators could launch a drone strike if they saw a group, for example, crossing back and forth over the Afghanistan-Pakistan border. In 2008, the Bush administration carried out 33 strikes.

Under Obama, the drone campaign has escalated rapidly. The number of strikes nearly doubled to 53 in 2009 and then doubled again to 118 in 2010. Former administration officials said the looser rules resulted in the killing of more civilians. Current administration officials insisted that Obama, in fact, tightened the rules on the use of drone strikes after taking office. They said strikes rose under Obama because improved technology and intelligence gathering created more opportunities for attacks than existed under Bush.

But as Pakistani public anger over the spiraling strikes grew, other diplomats expressed concern as well. The U.S. ambassador in Pakistan at the time, Anne Patterson, opposed several attacks, but the CIA ignored her objections. When Cameron Munter replaced Patterson in October 2010, he objected even more vigorously. On at least two occasions, CIA Director Leon Panetta dismissed Munter's protests and launched strikes, the Wall Street Journal later reported. One strike occurred only hours after Sen. John Kerry, head of the Senate Foreign Relations Committee, had completed a visit to Islamabad.

A March 2011 strike brought the debate to the White House. A day after Pakistani officials agreed to release CIA contractor Raymond Davis, the agency -- again over Munter's objections -- carried out a signature drone strike that the Pakistanis say killed four Taliban fighters and 38 civilians. Already angry about the Davis case, Pakistan's Army chief, Gen. Ashfaq Parvez Kayani, issued an unusual public statement, saying a group of tribal elders had been "carelessly and callously targeted with complete disregard to human life." U.S. intelligence officials dismissed the Pakistani complaints and insisted 20 militants had perished. "There's every indication that this was a group of terrorists, not a charity car wash in the Pakistani hinterlands," one official told the Associated Press.

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