Surprised by the vehemence of the official Pakistani reaction, national security advisor Tom Donilon questioned whether signature strikes were worthwhile. Critics inside and outside the U.S. government contended that a program that began as a carefully focused effort to kill senior al Qaeda leaders had morphed into a bombing campaign against low-level Taliban fighters. Some outside analysts even argued that the administration had adopted a de facto "kill not capture" policy, given its inability to close Bush's Guantánamo Bay prison and create a new detention system.

In April 2011, the director of Pakistan's intelligence service, Lt. Gen. Ahmed Shuja Pasha, visited Washington in an effort to repair the relationship, according to news accounts and former administration officials. Just after his visit, two more drone strikes occurred in the tribal areas, which Pasha took as a personal affront. In a rare concession, Panetta agreed to notify Pakistan's intelligence service before the United States carried out any strike that could kill more than 20 people.

In May, after the bin Laden raid sparked further anger among Pakistani officials, Donilon launched an internal review of how drone strikes were approved, according to a former administration official. But the strikes continued. At the end of May, State Department officials were angered when three missile strikes followed Secretary of State Hillary Clinton's visit to Pakistan.

As Donilon's review progressed, an intense debate erupted inside the administration over the signature strikes, according to the Journal. Adm. Mike Mullen, then chairman of the Joint Chiefs of Staff, said the strikes should be more selective. Robert Gates, then the defense secretary, warned that angry Pakistani officials could cut off supplies to U.S. troops in Afghanistan. Clinton warned that too many civilian casualties could strengthen opposition to Pakistan's weak, pro-American president, Asif Ali Zardari.

The CIA countered that Taliban fighters were legitimate targets because they carried out cross-border attacks on U.S. forces, according to the former official. In June, Obama sided with the CIA. Panetta conceded that no drone strike would be carried out when Pakistani officials visited Washington and that Clinton and Munter could object to proposed strikes. But Obama allowed the CIA director to retain final say.

Last November, the worst-case scenario that Mullen, Gates, and Clinton had warned of came to pass. After NATO airstrikes mistakenly killed 24 Pakistani soldiers on the Afghanistan-Pakistan border, Kayani demanded an end to all U.S. drone strikes and blocked supplies to U.S. troops in Afghanistan. At the same time, popular opposition to Zardari soared. After a nearly two-month lull that allowed militants to regroup, drone strikes resumed in the tribal areas this past January. But signature strikes are no longer allowed -- for the time being, according to the former senior official.

Among average Pakistanis, the strikes played out disastrously. In a 2011 Pew Research Center poll, 97 percent of Pakistani respondents who knew about the attacks said American drone strikes were a "bad thing." Seventy-three percent of Pakistanis had an unfavorable view of the United States, a 10 percentage point rise from 2008. Administration officials say the strikes are popular with Pakistanis who live in the tribal areas and have tired of brutal jihadi rule. And they contend that Pakistani government officials -- while publicly criticizing the attacks -- agree in private that they help combat militancy. Making the strikes more transparent could reduce public anger in other parts of Pakistan, U.S. officials concede. But they say some elements of the Pakistani government continue to request that the strikes remain covert.

For me, the bottom line is that both governments' approaches are failing. Pakistan's economy is dismal. Its military continues to shelter Taliban fighters it sees as proxies to thwart Indian encroachment in Afghanistan. And the percentage of Pakistanis supporting the use of the Pakistani Army to fight extremists in the tribal areas -- the key to eradicating militancy -- dropped from a 53 percent majority in 2009 to 37 percent last year. Pakistan is more unstable today than it was when Obama took office.

A similar dynamic is creating even worse results on the southern tip of the Arabian Peninsula. Long ignored by the United States, Yemen drew sudden attention after a suicide attack on the USS Cole killed 17 American sailors in the port of Aden in 2000. In 2002, the Bush administration carried out a single drone strike in Yemen that killed Abu Ali al-Harithi, an al Qaeda operative who was a key figure in orchestrating the Cole attack. In the years that followed, the administration shifted its attentions to Iraq, and militants began to regroup.

A failed December 2009 attempt by a militant trained in Yemen to detonate a bomb on a Detroit-bound airliner focused Obama's attention on the country. Over the next two years, the United States carried out an estimated 20 airstrikes in Yemen, most in 2011. In addition to killing al Qaeda-linked militants, the strikes killed dozens of civilians, according to Yemenis. Instead of decimating the organization, the Obama strikes have increased the ranks of al Qaeda in the Arabian Peninsula from 300 fighters in 2009 to more than 1,000 today, according to Gregory Johnsen, a leading Yemen expert at Princeton University. In January, the group briefly seized control of Radda, a town only 100 miles from the capital, Sanaa. "I don't believe that the U.S. has a Yemen policy," Johnsen told me. "What the U.S. has is a counterterrorism strategy that it applies to Yemen."

The deaths of bin Laden and many of his lieutenants are a step forward, but Pakistan and Yemen are increasingly unstable. Pakistan is a nuclear-armed country of 180 million with resilient militant networks; Yemen, an impoverished, failing state that is fast becoming a new al Qaeda stronghold. "They think they've won because of this approach," the former administration official said, referring to the administration's drone-heavy strategy. "A lot of us think there is going to be a lot bigger problems in the future."

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