But Pakistan’s military, which oversees the country’s security and foreign policy, has dug in its heels under public and internal pressure. It looks set to impede the U.S. military action against militant groups and hideouts inside Pakistan that is necessary for the Obama administration’s plans to start drawing down from Afghanistan.

On his visit to Islamabad last week, CIA chief Leon Panetta reportedly confronted the Army chief, Gen. Ashfaq Kayani, with evidence of Pakistan’s tipping off militant targets, specifically explosives experts who are part of the suicide-bombing factory line. Panetta is also said to have expressed concern for the safety of the five CIA informants, including a Pakistan Army major, who may have provided information on Osama bin Laden’s whereabouts. It is believed that these men have been detained by the military for questioning, and possible court-martial. In a terse press statement on Wednesday, the military denied any officers had been arrested.

Except that such rote denials are finding few takers, especially in Pakistan, where the old customary deference accorded to the military is gone, and its rank-and-file tensions are now out in the open. The issue of divided allegiances is not new. What is alarming is that they seem to run deeper than previously acknowledged. Husain Haqqani, author of Between Mosque and Military and currently Pakistan’s ambassador in Washington, points to the past for an explanation of the present challenge. “The years of jihad in Afghanistan [in the 1980s] and Kashmir [in the 1990s] have confused our officers and people,” he told The Daily Beast. “For many, ideology determines the worldview instead of the strategic reality.”

The reported, and since denied, arrests of CIA informants within the Army do not necessarily show diversity among the divided. Given the $50 million bounty on bin Laden’s head, it is unlikely that the alleged informants were operating out of ideological purity. This likelihood only raises more concerns about the integrity of commissioned personnel, including those tasked to safeguard the country’s growing nuclear arsenal. (Pakistani government and military officials insist security at the nuclear facilities is adequate.)

Kashmiri took his 313 Brigade into al Qaeda's camp and assisted in training Taliban fighters in Afghanistan and began targeting his former friends in the ISI. His teams killed at least one senior ISI officer. He was involved in an attempt to assassinate Musharraf in 2004. The United Nations credits him as a key player in the plot to murder former Prime Minister Benazir Bhutto in December 2007.

The Pakistani American David Headley, who has confessed to plotting the Mumbai terror attack in November 2008, says Kashmiri was his key contact in al Qaeda. The two worked on a plot to attack a Danish newspaper office in Copenhagen in 2009. That was foiled when the FBI arrested Headley, but Kashmiri continued planning to carry out Mumbai-style attacks in Europe. Another was foiled in Denmark at the end of 2010.

Kashmiri would have played an important role in helping al Qaeda recover from bin Laden's demise. He had key connections inside the Pakistani syndicate of terror groups.

Just last week one of Pakistan's best investigative reporters Syed Salam Shahzad was murdered after finishing a new book on al Qaeda in Pakistan. According to excerpts published in India and Pakistan, Shahzad had evidence Kashmiri may have been the real brains behind the Mumbai plot and hoped it would precipitate an Indo-Pakistani war that al Qaeda could exploit.

They may have concluded that a compound on the outskirts of an army town like Abbottabad would be the last place the Pakistanis would expect the al Qaeda leader to hide.

One of the main features of that war has been a domestic terrorism campaign inside the Pakistani heartland, whose primary targets have been Pakistani security forces, including the army and its intelligence service ISI. To take just one example, in December 2009, the son of the lieutenant general commanding Pakistani forces in the tribal areas and Khyber Pakhtunkhwa was killed in an attack on a mosque frequented by army families in Rawalpindi. He died along with a major general and 40 others, 16 of them children. Nor has ISI escaped lightly. Its headquarters in Lahore, Peshawar, and Multan have all been car bombed by al Qaeda affiliated terrorists, with considerable loss of life. Why would the Pakistan army extend protection to the leader of a group whose operatives had been actively engaged in committing terrorist attacks against it? And what possible strategic advantage would have justified the risk? It is easy enough to see why the Pakistanis support the Afghan Taliban. They see them as a hedge against an Indian alliance with the Karzai government once the U.S. has departed.

But what do they get from protecting Osama bin Laden? He was not just any terrorist, but the great bête noire of the United States, whose stated goal was to destroy America. Anyone protecting him would be certain to be regarded as an enemy of the United States. The Pakistanis must surely have realized that if Washington ever discovered they were protecting him, this would bring their relationship to an abrupt and highly confrontational end. This might still be the result if evidence of collaboration is found somewhere among the artifacts spirited out of the bin Laden compound by the Navy SEAL team. It is also useful to consider the matter from bin Laden’s perspective. He may have been evil but he was no dummy. Given the factors cited above, how likely is it that he would have trusted a Pakistan army offer to have him come stay with them in Abbottabad?

Another possibility is that the Pakistanis knew, or suspected, that bin Laden was holed up in the Abbottabad compound but decided to do nothing about it. There is a regrettable tendency among the people who rule Pakistan, civilian and military alike, to kick serious problems down the road and it is hard to conceive of a more serious problem than this. An argument can also be made that they would have been concerned about the domestic reaction to news that they had killed bin Laden themselves or turned him over to the United States. On a superficial level, bin Laden remained something of a folk hero to many Muslims, Pakistanis included. There would very likely have been demonstrations by religious radicals and a possible upsurge in terrorist attacks perpetrated by the Pakistani Taliban and its al Qaeda allies. But such events would be unlikely to pose a substantially increased threat. Protest demonstrations and terrorist attacks already constitute part of the background noise of day-to-day Pakistani life. Every significant jihadist and radical sectarian group in Pakistan save one, the Lashkar-e-Taiba, has already turned against the state.

The trial begins with BUD/S (basic underwater demolition/SEAL training) at the Naval Special Warfare Center in Coronado, California, an otherwise lovely island in San Diego Bay. On the "grinder," a black asphalt courtyard, would-be SEALs spend hours doing mass calisthenics. In the pool, they are "drown-proofed" by swimming with bound arms and legs. On the shore, they experience "surf torture" (official name: water immersion), a prolonged bob in the 60-degree Pacific Ocean, or are made to jump on and off a pier while being hosed down with cold water. After hours of this—literally—men begin to crack up, and a class of 100 can shrink by 10 percent in a few minutes. Those who stick it out end up as "sugar cookies," wet, blue-lipped men belly-flopping on the beach: "Up! Down! Up! Down!"

Gallery: Navy SEALs

• The Daily Beast's Complete Osama bin Laden Coverage

Then a whistle blows: Time for a four-mile run. Or time to retrieve a raft from a distant shed and support the 150-pound object—packed with paddles and gear—on your head, which ends up red and rubbed bald. Or time to go into the surf for a 17-mile lap around the island, or to practice landing on a patch of jagged shore. The most sacred rite of passage, the peak of SEAL training, is known as "Hell Week," a five-day regime of simulated battle stress—and a total of four hours of sleep. Some would-be SEALs turn to gallows humor to endure the pain, telling themselves “the only easy day was yesterday.” Others call their megaphone-wielding instructor “The Antichrist.” Men can quit at any time by ringing a bell, and historically, two out of three do so.

• The Daily Beast's Complete Osama bin Laden Coverage

The SEALs originated as "frogmen" clearing beaches during World War II, moved on to bridge demolition during Korea, and gained fame (along with the SEAL name) during Vietnam. But the modern SEALs were born in the aftermath of the Iran hostage crisis as a specialized counterterrorism force. The initial results were underwhelming: Four drowned during the invasion of Grenada in 1983, a team failed to save a kidnapped CIA station chief in Beirut in 1985, and by 1987 the whole division was wracked with fraud (including cases of guys stealing scuba equipment). The 1990s were scarcely better, as SEAL units "were never used even once to track down terrorists who had taken American lives," according to a 2004 study by Richard H. Schultz Jr., the director of the International Security Studies Program at Tufts University.

The main reason, he says, was risk-aversion: The Clinton administration didn't want to contemplate another Mogadishu, where more than a dozen Special Ops soldiers were killed in 1993. That calculation held, Schultz argues, even as al Qaeda bombed the World Trade Center, struck two U.S. embassies in East Africa, and tried to sink the USS Cole in Yemen in 2000. After the September 11th attacks, however, the Bush administration began to lean heavily on so-called hunter-killer teams dispatched to kill terrorists abroad. And President Obama has continued to do so-—some say even more so than his predecessor.

The upshot: an estimated 2,000 dead members of al Qaeda, "a significant portion" of them deep-sixed by the SEALs, says Schultz.

Tony Dokoupil is a staff writer and editor at Newsweek.

• The Daily Beast's Complete Osama bin Laden Coverage

Yet hardly anybody in this country has complained about Obama’s use of covert operations on such a broad scale—certainly not the human-rights advocates, who have been largely silent about the forces in Pakistan. As Tom Malinowski, the Washington director of Human Rights Watch, told me in the fall, it has been easier for Obama to justify these clandestine actions “because he’s a Democrat, and he is seen as a champion of civil liberties and the rule of law.”

The seduction of targeted warfare, whether carried out by drone attacks or by Special Operations, is clear: The strikes are quick and surgical, involving only a handful of Americans, and yield results, as we saw so spectacularly in Osama bin Laden’s case. The premise of targeted warfare rests on the assumption of good data, however, and until now that has been in short supply. More than 1,340 people have been killed in Obama’s pursuit of bin Laden and other terrorists in Pakistan; at least 200 of them were not militants, according to the New America Foundation, and nearly all of those who were classified as Taliban, al Qaeda, or other terrorists were low-level fighters who posed little danger to Americans.

As one legal expert has written, it may be better to kill them from afar so that Americans are not faced with the messy prospect of a terrorist who wants to surrender. Administration officials told reporters that bin Laden resisted the U.S. forces in a firefight that erupted after the helicopter raid Sunday, but most terrorists will try to give themselves up. Suicide bombers aside, the individuals who support al Qaeda and its principles, and particularly those at the upper levels of the organization, are by and large in no hurry to die. A former CIA operative who hunted down dozens of al Qaeda fighters in Pakistan after the 9/11 attacks told me that most of them were illiterate teenage boys from poor families. When they were caught, he said, a lot of them didn’t fight back—instead, they just cried.

It was hard to see how much good any of this did, at least in terms of protecting U.S. national security, until the biggest target, bin Laden, was taken out.