...

Pakistan has been a nuclear power for two decades, and has an estimated eighty to a hundred warheads, scattered in facilities around the country. The success of the latest attacks raised an obvious question : Are the bombs safe ?

...

current and former officials said in interviews in Washington and Pakistan that [Obama’s] Administration has been negotiating highly sensitive understandings with the Pakistani military. These would allow specially trained American units to provide added security for the Pakistani arsenal in case of a crisis. At the same time, the Pakistani military would be given money to equip and train Pakistani soldiers and to improve their housing and facilities-goals that General Ashfaq Parvez Kayani, the chief of the Pakistan Army, has long desired.

...

The ongoing consultation on nuclear security between Washington and Islamabad intensified after the announcement in March of President Obama’s so-called Af-Pak policy, which called upon the Pakistan Army to take more aggressive action against Taliban enclaves inside Pakistan. I was told that the understandings on nuclear coöperation benefitted from the increasingly close relationship between Admiral Michael Mullen, the chairman of the Joint Chiefs of Staff, and General Kayani, his counterpart, although the C.I.A. and the Departments of Defense, State, and Energy have also been involved. (All three departments declined to comment for this article. The national-security council and the C.I.A. denied that there were any agreements in place.)

...

the Pakistani official said, “both sides are lying to each other.” The information that the Pakistanis handed over was not as complete as the Americans believed. “We haven’t told you anything that you don’t know,” he said. The Americans didn’t realize that Pakistan would never cede control of its arsenal : “If you try to take the weapons away, you will fail.”

...

Safeguards have been built into the system. Pakistani nuclear doctrine calls for the warheads (containing an enriched radioactive core) and their triggers (sophisticated devices containing highly explosive lenses, detonators, and krytrons) to be stored separately from each other and from their delivery devices (missiles or aircraft).

...

In an actual crisis, would the Pakistanis give an American team direct access to their arsenal ? An adviser to the Pentagon on counterinsurgency said that some analysts suspected that the Pakistani military had taken steps to move elements of the nuclear arsenal “out of the count”-to shift them to a storage facility known only to a very few-as a hedge against mutiny or an American or Indian effort to seize them. “If you thought your American ally was telling your enemy where the weapons were, you’d do the same thing,” the adviser said.

...

The Obama Administration has had difficulty coming to terms with how unhappy many Pakistanis are with the United States. Secretary of State Clinton, during her three-day “good-will visit” to Pakistan, late last month, seemed taken aback by the angry and, at times, provocative criticism of American policies that dominated many of her public appearances, and responded defensively.

...

[One] article quoted Major General John Custer as saying, “The older military leaders love us. They understand American culture and they know we are not the enemy.” The General’s assessment provoked a barrage of e-mail among American officers with experience in Pakistan, and a former member of a Special Forces unit provided me with copies. “The fact that a two-star would make a statement [like] that . . . is at best naïve and actually pure bullshit,” a senior Special Forces officer on duty in Pakistan wrote.

...

Sultan Amir Tarar, known to many as Colonel Imam, is the archetype of the disillusioned Pakistani officer. Tarar spent eighteen years with the I.S.I. in Afghanistan, most of them as an undercover operative. In the mujahideen war against the Soviet Union, in the eighties, he worked closely with C.I.A. agents, and liked the experience. ... Tarar, who retired in 1995 and has a son in the Army, believed-as did many Pakistani military men-that the American campaign to draw Pakistan deeper into the war against the Taliban would backfire. “The Americans are trying to rent out their war to us,” he said. If the Obama Administration persists, “there will be an uprising here, and this corrupt government will collapse. Every Pakistani will then be his own nuclear bomb-a suicide bomber,” Tarar said. “The longer the war goes on, the longer it will spill over in the tribal territories, and it will lead to a revolutionary stage.

...

Speaking to Tarar and other officers gave a glimpse of the acrimony at the top of the Pakistani government, which has complicated the nuclear equation. Tarar spoke bitterly about the position that General Kayani found himself in, carrying out the “corrupt” policies of the Americans and of Zardari, while Pakistan’s soldiers “were fighting gallantly in Swat against their own people.”

...

During my stay in Pakistan-my first in five years-there were undeniable signs that militancy and the influence of fundamentalist Islam had grown. In the past, military officers, politicians, and journalists routinely served Johnnie Walker Black during our talks, and drank it themselves. This time, even the most senior retired Army generals offered only juice or tea, even in their own homes. Officials and journalists said that soldiers and middle-level officers were increasingly attracted to the preaching of Zaid Hamid, who joined the mujahideen and fought for nine years in Afghanistan. On CDs and on television, Hamid exhorts soldiers to think of themselves as Muslims first and Pakistanis second. He claims that terrorist attacks in Mumbai last year were staged by India and Western Zionists, aided by the Mossad. Another proselytizer, Dr. Israr Ahmed, writes a column in the Urdu press in which he depicts the Holocaust as “divine punishment,” and advocates the extermination of the Jews. He, too, is said to be popular with the officer corps.

...

A senior Obama Administration official brought up Hizb ut-Tahrir, a Sunni organization whose goal is to establish the Caliphate. “They’ve penetrated the Pakistani military and now have cells in the Army,” he said. (The Pakistan Army denies this.) In one case, according to the official, Hizb ut-Tahrir had recruited members of a junior officer group, from the most élite Pakistani military academy, who had been sent to England for additional training.

“Where do these guys get socialized and exposed to Islamic evangelism and the fundamentalism narrative ?” the Obama Administration official asked. “In services every Friday for Army officers, and at corps and unit meetings where they are addressed by senior commanders and clerics.”