The Ally From Hell

Shortly after American Navy SEALs raided the Pakistani city of Abbottabad in May and killed Osama bin Laden, General Ashfaq Kayani, the Pakistani chief of army staff, spoke with Khalid Kidwai, the retired lieutenant general in charge of securing Pakistan’s nuclear arsenal. Kidwai, who commands a security apparatus called the Strategic Plans Division (SPD), had been expecting Kayani’s call.

General Kayani, the most powerful man in a country that has only a simulacrum of civilian leadership, had been busy in the tense days that followed the bin Laden raid: he had to assure his American funders (U.S. taxpayers provide more than $2 billion in annual subsidies to the Pakistani military) that the army had no prior knowledge of bin Laden’s hideout, located less than a mile from Pakistan’s preeminent military academy; and at the same time he had to subdue the uproar within his ranks over what was seen as a flagrant violation of Pakistan’s sovereignty by an arrogant Barack Obama. But he was also anxious about the safety of Pakistan’s nuclear weapons, and he found time to express this worry to General Kidwai.

Much of the world, of course, is anxious about the security of Pakistan’s nuclear weapons, and for good reason: Pakistan is an unstable and violent country located at the epicenter of global jihadism, and it has been the foremost supplier of nuclear technology to such rogue states as Iran and North Korea. It is perfectly sensible to believe that Pakistan might not be the safest place on Earth to warehouse 100 or more nuclear weapons. These weapons are stored on bases and in facilities spread across the country (possibly including one within several miles of Abbottabad, a city that, in addition to having hosted Osama bin Laden, is home to many partisans of the jihadist group Harakat-ul-Mujahideen). Western leaders have stated that a paramount goal of their counterterrorism efforts is to keep nuclear weapons out of the hands of jihadists.

“The single biggest threat to U.S. security, both short-term, medium-term, and long-term, would be the possibility of a terrorist organization obtaining a nuclear weapon,” President Obama said last year at an international nuclear-security meeting in Washington. Al-Qaeda, Obama said, is “trying to secure a nuclear weapon—a weapon of mass destruction that they have no compunction at using.”

Pakistan would be an obvious place for a jihadist organization to seek a nuclear weapon or fissile material: it is the only Muslim-majority state, out of the 50 or so in the world, to have successfully developed nuclear weapons; its central government is of limited competence and has serious trouble projecting its authority into many corners of its territory (on occasion it has difficulty maintaining order even in the country’s largest city, Karachi); Pakistan’s military and security services are infiltrated by an unknown number of jihadist sympathizers; and many jihadist organizations are headquartered there already.

“There are three threats,” says Graham Allison, an expert on nuclear weapons who directs the Belfer Center for Science and International Affairs at Harvard. The first is “a terrorist theft of a nuclear weapon, which they take to Mumbai or New York for a nuclear 9/11. The second is a transfer of a nuclear weapon to a state like Iran. The third is a takeover of nuclear weapons by a militant group during a period of instability or splintering of the state.” Pakistani leaders have argued forcefully that the country’s nuclear weapons are secure. In times of relative quiet between Pakistan and India (the country that would be the target of a Pakistani nuclear attack), Pakistani officials claim that their weapons are “de-mated”—meaning that the warheads are kept separate from their fissile cores and their delivery systems. This makes stealing, or launching, a complete nuclear weapon far more difficult. Over the past several years, as Pakistan has suffered an eruption of jihadist terrorism, its officials have spent a great deal of time defending the safety of their nuclear program. Some have implied that questions about the safety of the Pakistani nuclear arsenal are motivated by anti-Muslim prejudice. Pervez Musharraf, Pakistan’s former army chief and president, who created the SPD, told The Atlantic in a recent interview: “I think it’s overstated that the weapons can get into bad hands.” Referring to Pakistan’s main adversary, India, he said, “No one ever speaks of the dangers of a Hindu bomb.”

Current officials of the Pakistani government are even more adamant on the issue. In an interview this summer in Islamabad, a senior official of the Inter-Services Intelligence directorate (ISI), the Pakistani military’s spy agency, told The Atlantic that American fears about the safety of Pakistan’s nuclear weapons were entirely unfounded. “Of all the things in the world to worry about, the issue you should worry about the least is the safety of our nuclear program,” the official said. “It is completely secure.” He went on to say, “It is in our interest to keep our bases safe as well. You must trust us that we have maximum and impenetrable security. No one with ill intent can get near our strategic assets.”

Like many statements made by Pakistan’s current leaders, this one contained large elements of deceit. At least six facilities widely believed to be associated with Pakistan’s nuclear program have already been targeted by militants. In November 2007, a suicide bomber attacked a bus carrying workers to the Sargodha air base, which is believed to house nuclear weapons; the following month, a school bus was attacked outside Kamra air base, which may also serve as a nuclear storage site; in August 2008, Pakistani Taliban suicide bombers attacked what experts believe to be the country’s main nuclear-weapons-assembly depot in Wah cantonment. If jihadists are looking to raid a nuclear facility, they have a wide selection of targets: Pakistan is very secretive about the locations of its nuclear facilities, but satellite imagery and other sources suggest that there are at least 15 sites across Pakistan at which jihadists could find warheads or other nuclear materials. (See map on opposite page.)

It is true that the SPD is considered to be a highly professional organization, at least by Pakistani-government standards of professionalism. General Kidwai, its leader, is well regarded by Western nuclear-security experts, and the soldiers and civilians he leads are said by Pakistani spokesmen to be screened rigorously for their probity and competence, and for signs of political or religious immoderation. The SPD, Pakistani officials say, keeps careful watch over behavioral changes in its personnel; employees are investigated thoroughly for ties to extremists, and to radical mosques, and for changes in their lifestyle and income. The SPD also is believed to maintain “dummy” storage sites that serve to divert attention from active ones.

Pakistani spokesmen say the SPD is also vigilant in its monitoring of the civilian scientists—there are as many as 9,000, including at least 2,000 who possess “critical knowledge” of weapons manufacture and maintenance, according to two sources in Pakistan—working in their country’s nuclear complexes, a watchfulness deemed necessary after disclosures that two retired Pakistani nuclear scientists of pronounced jihadist sympathies had met with Osama bin Laden in the summer of 2001.

Some American intelligence experts question Pakistan’s nuclear vigilance. Thomas Fingar, a former chairman of the National Intelligence Council and deputy director of national intelligence under President George W. Bush, said it is logical that any nuclear-weapons state would budget the resources necessary to protect its arsenal—but that “we do not know that this is the case in Pakistan.” The key concern, Fingar says, is that “we do not know if what the military has done is adequate to protect the weapons from insider threats, or if key military units have been penetrated by extremists. We hope the weapons are safe, but we may be whistling past the graveyard.”

Also see:



Nuclear Pakistan
A map of sites that are known to be, or suspected to have been, associated with the country’s nuclear program.

There is evidence to suggest that neither the Pakistani army, nor the SPD itself, considers jihadism the most immediate threat to the security of its nuclear weapons; indeed, General Kayani’s worry, as expressed to General Kidwai after Abbottabad, was focused on the United States. According to sources in Pakistan, General Kayani believes that the U.S. has designs on the Pakistani nuclear program, and that the Abbottabad raid suggested that the U.S. has developed the technical means to stage simultaneous raids on Pakistan’s nuclear facilities.

In their conversations, General Kidwai assured General Kayani that the counterintelligence branch of the SPD remained focused on rooting out American and Indian spies from the Pakistani nuclear-weapons complex, and on foiling other American espionage methods. The Pakistani air force drills its pilots in ways of intercepting American spy planes; the Pakistani military assumes (correctly) that the U.S. devotes many resources to aerial and satellite surveillance of its nuclear sites.

In their post-Abbottabad discussion, General Kayani wanted to know what additional steps General Kidwai was taking to protect his nation’s nuclear weapons from the threat of an American raid. General Kidwai made the same assurances he has made many times to Pakistan’s leaders: Pakistan’s program was sufficiently hardened, and dispersed, so that the U.S. would have to mount a sizable invasion of the country in order to neutralize its weapons; a raid on the scale of the Abbottabad incursion would simply not suffice.

Still, General Kidwai promised that he would redouble the SPD’s efforts to keep his country’s weapons far from the prying eyes, and long arms, of the Americans, and so he did: according to multiple sources in Pakistan, he ordered an increase in the tempo of the dispersal of nuclear-weapons components and other sensitive materials. One method the SPD uses to ensure the safety of its nuclear weapons is to move them among the 15 or more facilities that handle them. Nuclear weapons must go to the shop for occasional maintenance, and so they must be moved to suitably equipped facilities, but Pakistan is also said to move them about the country in an attempt to keep American and Indian intelligence agencies guessing about their locations.

Nuclear-weapons components are sometimes moved by helicopter and sometimes moved over roads. And instead of moving nuclear material in armored, well-defended convoys, the SPD prefers to move material by subterfuge, in civilian-style vehicles without noticeable defenses, in the regular flow of traffic. According to both Pakistani and American sources, vans with a modest security profile are sometimes the preferred conveyance. And according to a senior U.S. intelligence official, the Pakistanis have begun using this low-security method to transfer not merely the “de-mated” component nuclear parts but “mated” nuclear weapons. Western nuclear experts have feared that Pakistan is building small, “tactical” nuclear weapons for quick deployment on the battlefield. In fact, not only is Pakistan building these devices, it is also now moving them over roads.

What this means, in essence, is this: In a country that is home to the harshest variants of Muslim fundamentalism, and to the headquarters of the organizations that espouse these extremist ideologies, including al-Qaeda, the Haqqani network, and Lashkar-e-Taiba (which conducted the devastating terror attacks on Mumbai three years ago that killed nearly 200 civilians), nuclear bombs capable of destroying entire cities are transported in delivery vans on congested and dangerous roads. And Pakistani and American sources say that since the raid on Abbottabad, the Pakistanis have provoked anxiety inside the Pentagon by increasing the pace of these movements. In other words, the Pakistani government is willing to make its nuclear weapons more vulnerable to theft by jihadists simply to hide them from the United States, the country that funds much of its military budget.

The nuclear shell game played by Pakistan is one more manifestation of the slow-burning war between the U.S. and Pakistan. The national-security interests of the two countries are often in almost perfect opposition, but neither Pakistan nor the U.S. has historically been able or willing to admit that they are locked in conflict, because they are also dependent on each other in crucial ways: the Pakistani military still relies on American funding and American-built weapons systems, and the Obama administration, in turn, believes Pakistani cooperation is crucial to the achievement of its main goal of defeating the “al-Qaeda core,” the organization now led by bin Laden’s former deputy, Ayman al-Zawahiri. The U.S. also moves much of the matériel for its forces in Afghanistan through Pakistan, and must cross Pakistani airspace to fly from Arabian Sea–based aircraft carriers to Afghanistan. (In perhaps the most bizarre expression of this dysfunctional relationship, Osama bin Laden’s body was flown out of Pakistan by the American invasion force, which did not seek Pakistani permission and was prepared to take Pakistani anti-aircraft fire—but then, hours later, bin Laden’s body was flown back over Pakistan on a regularly routed American military flight between Bagram Air Base in Afghanistan and the aircraft carrier Carl Vinson, in the Arabian Sea.)

Public pronouncements to the contrary, very few figures in the highest ranks of the American and Pakistani governments suffer from the illusion that their countries are anything but adversaries, whose national-security interests clash radically and, it seems, permanently. Pakistani leaders obsess about what they view as the existential threat posed by nuclear-armed India, a country that is now a strategic ally of the United States. Pakistani policy makers The Atlantic interviewed in Islamabad and Rawalpindi this summer uniformly believe that India is bent on drawing Afghanistan into an alliance against Pakistan. (Pervez Musharraf said the same thing during an interview in Washington.) Many of Pakistan’s leaders have long believed that the Taliban, and Taliban-like groups, are the most potent defenders of their interests in Afghanistan.

The level of animosity between Islamabad and Washington has spiked in the days since the raid on Abbottabad. Many Americans, in and out of official life, do not believe Pakistan’s government when it says that no high-ranking official knew of bin Laden’s presence in Abbottabad; Pakistanis, for their part, see the raid on bin Laden’s hideout—conducted without forewarning—as a gross insult. Since the raid, the ISI has waged a street-level campaign against the CIA, harassing its employees and denying visas to its officers.

While the hostility and distrust have increased of late, the relationship between the two countries has been shot through with rage, resentment, and pretense for years. The relationship has survived as long as it has only because both countries have chosen to pretend to believe the lies they tell each other.

Pakistan’s lies, in particular, have been abundant. The Pakistani government has willfully misled the U.S. for more than 20 years about its support for terrorist organizations, and it willfully misleads the American government when it asserts, against the evidence, that “rogue elements” within the ISI are responsible for the acts of terrorism against India and U.S. forces in Afghanistan. Most American officials are at this late stage convinced that there are no “rogue elements” of any size or importance in the ISI; there are only the ISI and the ISI assets that the ISI (with increasing implausibility) denies having. (The ISI’s S Wing, the branch of the service that runs anti-India activities, among other things, is said to have a very potent “alumni association,” in the words of Stephen P. Cohen, a leading American scholar of Pakistan based at the Brookings Institution.) A particular challenge the ISI poses is that while it funds and protects various jihadist groups, these groups often pick their own targets and the timing of their attacks. The ISI has worked for years against American interests—not only against American interests in Afghanistan, but against the American interest in defeating particular jihadist networks, even while it was also working with the Americans against other jihadist organizations.

“The problem with Pakistan is that they still differentiate between ‘good’ terrorists and ‘bad’ terrorists,” Mike Rogers, the Michigan Republican who chairs the House Intelligence Committee, told The Atlantic in October.

The ISI provides the U.S. with targeting information about certain jihadists—but only about those jihadists perceived to threaten the Pakistani state, such as members of the so-called Pakistani Taliban (the Tehrik-i-Taliban Pakistan) and al-Qaeda. At one time, the ISI was on friendlier terms with al-Qaeda’s leaders. According to the report of the 9/11 Commission, the ISI reportedly played matchmaker in the 1990s by bringing together the Taliban and al-Qaeda, hoping to create an umbrella group that would train fighters for anti-India operations in the disputed territory of Kashmir. The 9/11 plot was developed at the training camps jointly maintained by al-Qaeda and the Taliban. But when Pakistan, under General Musharraf, formally (though, as it turns out, less than completely) aligned itself with America after the September 11 attacks, al-Qaeda turned against the Pakistani government. In an interview this past summer, Musharraf said the goal of Pakistan should be to “wean the Pashtuns”—the ethnic group that supplies the Taliban organizations in both Afghanistan and Pakistan with their leaders and foot soldiers—from radicalism, but Musharraf himself has condemned terrorism on the one hand while encouraging Kashmiri extremists on the other.

The leaders of Lashkar-e-Taiba (the “Army of the Pure”), which has launched attacks against India, including the ferocious Mumbai attacks of November 2008, live openly in Pakistan—the organization maintains a 200-acre compound outside Lahore, and has offices in many major cities—and evidence gathered by the U.S. and India strongly suggests a direct ISI hand in the Mumbai attacks, among others. The would-be Times Square bomber, the Pakistani-American Faisal Shahzad, was trained in a militant camp in Pakistan’s tribal area. The past two U.S. National Intelligence Estimates on Pakistan—which represent the consensus views of America’s 16 spy agencies—concluded with a high degree of certainty that Pakistani support for jihadist groups has increased over the past several years.

The ISI also helps foment anti-Americanism inside Pakistan. American and Pakistani sources allege that the ISI pays journalists in the Pakistani press, most of which is moderately to virulently anti-American, to write articles hostile to the United States. An American visitor to Pakistan can easily see that a particular narrative has been embedded in the country’s collective psyche. This narrative holds that the U.S. favors India, punishes Pakistan unjustifiably, and periodically abandons Pakistan when American policy makers feel the country is not useful. “America is a disgrace because it turns on its friends when it has no use for them,” says General Aslam Beg, a retired chief of staff of the Pakistani army, in an efficient summation of the dominant Pakistani narrative. A Pew poll taken after the Abbottabad raid found that 69 percent of Pakistanis view the U.S. as “more of an enemy”; only 6 percent see the U.S. as “more of a partner.”

Although the U.S. did turn away from the region after the Soviet defeat in Afghanistan, and put renewed pressure on Pakistan over its nuclear program, the story is more complicated than that. A Pakistan expert at Georgetown University, C. Christine Fair, argues that Pakistan should expect American support to flag, given its long history of using militants to advance its interests in India and Afghanistan. “Pakistanis need to be held accountable for their decisions, and Americans and Pakistanis alike need to stop indulging in revisionist history that supports the incessant narrative of Pakistani victimhood,” Fair says. For example, Pakistanis frequently note that the United States did not support Pakistan in its wars with India even though the two states were treaty partners. On this point, Fair says, “We cut off arms supplies in 1965 to Pakistan because it started the war with India by using regular military personnel disguised as mujahideen. Pakistan was a treaty partner with the U.S. at the time—but what treaty says an alliance member has to supply another when it undertakes an act of unprovoked aggression?” In 1971, Fair says, “the Pakistanis were angry at the U.S. again, for not bailing them out from another war they started against India.”

Pakistani leaders also tell untruths when they assert that their military and security organizations are immune to radical influence. The ISI senior official The Atlantic interviewed in Islamabad in July made such an assertion: “I have seen no significant radicalization of any of our men in uniform. This is simply a lie,” he said. But a body of evidence suggests otherwise. Sympathy for jihadist-oriented groups among at least some Pakistani military men has been acknowledged for years, even inside Pakistan; recently a brigadier, Ali Khan, was arrested for allegedly maintaining contact with a banned extremist organization. While we were reporting this story, militants invaded a major Pakistani naval base near Karachi, blowing up two P-3C Orion surveillance planes and killing at least 10 people on the base. Pakistani security forces required 15 hours to regain control of the base. Experts believe that nuclear-weapon components were stored nearby. In a series of interviews, several Pakistani officials told The Atlantic that investigators believe the militants had help inside the base. A retired Pakistani general with intelligence experience says, “Different aspects of the military and security services have different levels of sympathy for the extremists. The navy is high in sympathy.”

In May, Pakistani security forces rushed to defend a Karachi naval base under attack by militants. Nuclear components were believed to be housed nearby. (Mohammed/Polaris)

The American lies about this tormented relationship are of a different sort. The U.S. government has lied to itself, and to its citizens, about the nature and actions of successive Pakistani governments. Pakistani behavior over the past 20 years has rendered the State Department’s list of state sponsors of terrorism effectively meaningless. The U.S. currently names four countries as state sponsors of terror: Sudan, Iran, Syria, and Cuba. American civilian and military officials have for years made the case, publicly and privately, that Pakistan is a state sponsor of terrorism—yet it has never been listed as such. In the last 12 months of the presidency of George H. W. Bush, for example, Secretary of State James Baker wrote a letter to the Pakistani prime minister, Nawaz Sharif, accusing Pakistan of supporting Muslim terrorists in Indian-administered Kashmir, as well as Sikh terrorists operating inside India. “We have information indicating that [the ISI] and others intend to continue to provide material support to groups that have engaged in terrorism,” the letter read. At this same time, a talking-points memo read to Pakistani leaders by Nicholas Platt, who was then the American ambassador to Pakistan, asserted, “Our information is certain.” The memo went on: “Please consider the serious consequences [to] our relationship if this support continues. If this situation persists, the Secretary of State may find himself required by law to place Pakistan on the state sponsors of terrorism list.”

The Baker threat caused a crisis inside the Pakistani government. In his book Pakistan: Between Mosque and Military, Husain Haqqani, the current Pakistani ambassador to Washington, writes that Javed Nasir, who was the ISI chief during this episode, told Prime Minister Sharif, “We have been covering our tracks so far and will cover them even better in the future.” The crisis was resolved, temporarily, when Nasir was removed as ISI chief the following year.

Similar crises have erupted with depressing frequency. In 1998, when the Clinton administration decided, in response to attacks by al-Qaeda on the American embassies in Kenya and Tanzania, to launch submarine-based missiles at al-Qaeda camps in Taliban-controlled Afghanistan in the hope of killing bin Laden, it faced a quandary: the missiles would have to fly over either Iran or Pakistan. Iran was not an option; it would label such a missile launch an aggressive act, and perhaps respond accordingly. But the administration, according to General Hugh Shelton, who was then the chairman of the Joint Chiefs of Staff, did not want to let Pakistan know in advance, for fear that the ISI would warn its allies in Afghanistan. A surprised Pakistan, however, might also misinterpret the missile launch as the beginning of an Indian attack. So Shelton dispatched his deputy to Islamabad to dine with the Pakistan army’s chief of staff on the night of the attack, to let him know, as the missiles were flying, that they were not launched from India. (Bin Laden was not at the al-Qaeda camp when the cruise missiles hit—but, tellingly, five ISI agents were. They were killed, as were a group of Kashmiri militants.)

Shortly after the 9/11 attacks, President Bush gave Pakistan’s then-president, Musharraf, an option: join the war on terror, or become one of its targets. Musharraf chose the first option. Over the next several years, the ISI cooperated with the U.S. in an intermittently sincere way, but the relationship soon returned to its dysfunctional state.

According to a secret 2006 U.S. National Intelligence Estimate on Afghanistan, “Available evidence strongly suggests that [the ISI] maintains an active and ongoing relationship with certain elements of the Taliban.” A 2008 National Intelligence Estimate concluded that the ISI was providing “intelligence and financial support to insurgent groups—especially the Jalaluddin Haqqani network out of Miram Shah, North Waziristan—to conduct attacks against Afghan government, [International Security Assistance Force], and Indian targets.” By late 2006, according to the intelligence historian Matthew Aid, who documents the dysfunctional relationship between the ISI and the CIA in his forthcoming book, Intel Wars, the U.S. had reliable intelligence indicating that Jalaluddin Haqqani and another pro-Taliban Afghan warlord, Gulbuddin Hekmatyar, were being given financial assistance by the ISI (which of course receives substantial financial assistance from the United States).

During nearly every meeting over the years between Pakistani military and intelligence chiefs and their American counterparts, the Pakistanis were “read the riot act”—a phrase that recurs with striking frequency in descriptions of these meetings. Each time, the Pakistanis denied everything. In one meeting several years ago, American intelligence officials asked Pakistani leaders to shut down the so-called Quetta Shura, the ruling council of those Taliban members associated with the former Afghan leader Mullah Muhammad Omar. Quetta is the capital of the Pakistani province of Baluchistan, and the Quetta Shura, according to numerous accounts, had its headquarters not far from a Pakistani army division headquarters there. But General Kayani, who was then the head of the ISI, looked puzzled, and “acted like he’d never heard of the Quetta Shura,” according to a source who was briefed on the meeting.

In 2008 Mike McConnell, who was then President Bush’s director of national intelligence, confronted the ISI chief, General Ahmed Shuja Pasha, with evidence that the ISI was tipping off jihadists so that they could escape in advance of American attacks against them. According to sources familiar with the conversation, McConnell accused Pakistan of not doing everything it could to rein in the Pakistani Taliban; he asserted that American intelligence had concluded that most Pakistani assets were still deployed against India. “How dare you tell me how our forces are deployed?,” Pasha said to McConnell. McConnell then provided Pasha with evidence to back up his assertion.

Meanwhile American generals, briefing Congress and officials of the Bush and Obama administrations, gave repeated assurances that they had developed the sort of personal relationships with Pakistani military leaders that would lead to a more productive alliance. Admiral Michael Mullen, who stepped down as chairman of the Joint Chiefs of Staff in late September, invested a great deal of time in his relationship with General Kayani. But eventually Mullen’s patience was exhausted; days before his retirement, Mullen finally broke with Kayani, publicly accusing the Pakistani army of supporting America’s enemies in Afghanistan. In his final appearance before the Senate Armed Services Committee, on September 22, Mullen said that ISI-supported operatives of the Haqqani network had conducted a recent attack on the American Embassy in Kabul. “The Haqqani network acts as a veritable arm of Pakistan’s Inter-Services Intelligence agency,” he said.

After Mullen’s explosive testimony, the Obama administration made only a desultory attempt to walk back his statement, and there are indications that the administration had already been recalibrating the way it deals with Pakistani dissembling. In April, General Pasha, the head of the ISI, visited Leon Panetta, who was then the director of the CIA, at the agency’s headquarters outside Washington. According to a source who was briefed on the meeting, Panetta upheld an American tradition: he “read Pasha the riot act.” The message conveyed by Panetta to Pasha and the ISI was: “If you don’t stop your relations with the Haqqani network in particular, but also other groups, the U.S. will be forced to rethink its entire relationship with the Pakistani military.”

Admiral Mullen had been even more shocked by the murder last May of Saleem Shahzad, a Pakistani journalist. Shahzad, who maintained close contact with various jihadist leaders, had angered ISI leaders with his reporting, according to The New Yorker. Not long after the killing, Admiral Mullen took the unprecedented step of stating publicly that Shahzad’s death had been “sanctioned by the government” of Pakistan. “I have not seen anything to disabuse the report that the government knew about this,” he said. In fact, he had seen reliable intelligence proving that the top leaders of the Pakistani army and ISI had ordered the murder. The New Yorker reported that the order to kill Shahzad came from an officer on General Kayani’s staff. Sources we spoke with say the order was passed directly to General Pasha, the head of the ISI. According to one of the sources, an official with knowledge of the intelligence, Pasha was told to “deal with it” and “take care of the problem.” According to this source, Mullen was horrified that his Pakistani interlocutors of many years had been involved in orchestrating the killing of a journalist. “It struck a visceral chord with him,” the source told The Atlantic, recalling that Mullen had slammed his desk and said, “This is old school.”

The ISI has strenuously denied any involvement in the Shahzad murder. “There will be no statements on these unsubstantiated matters,” Commodore Zafar Iqbal, an ISI spokesman, said when asked for comment. Another high-ranking official of the ISI said during an extended conversation in Islamabad: “That is an absolutely false allegation. The government of Pakistan had nothing to do with the unfortunate death.” Talking at length with this senior ISI official provided a reporter with a sense of what life must be like for American officials who work regularly with that organization. When asked about the allegation that Lashkar-e-Taiba operates under the protection of the ISI, he said, “We don’t have anything to do with that, not at all.” What about the Mumbai attacks? “We had nothing to do with that. To say that the ISI was involved in Mumbai is really unfair.” What about the Haqqani network and its attacks on U.S. forces in Afghanistan? “The Haqqani network is something completely separate from us.” When asked if the country’s various security services were equal to the task of protecting civilians from Pakistan’s large assortment of jihadist groups, he gave an enthusiastic yes.

The conversation took place in the restaurant of the Serena Hotel in Islamabad. The Serena has become an armed fortress: cars are banned from the hotel entrance; security guards and anti-terror police patrol the perimeter of the hotel, which is surrounded by razor wire; and guests and visitors must pass through three separate security checks before being allowed into the lobby, which is itself watched by plainclothes ISI agents. These various precautions would seem to suggest that Islamabad is itself not entirely secure. It was noted that in neighboring Rawalpindi, one of Pakistan’s so-called garrison cities (Abbottabad is another), the general headquarters of the Pakistani army itself came under sustained attack by the Taliban in 2009. Doesn’t all of this suggest that Pakistan is not a secure country?, the ISI official was asked. “Nonsense,” he replied. “Americans are much too concerned about the stability and safety of Pakistan.”

What really worries American strategic thinkers is less the relative dangerousness of the streets and hotels of Islamabad and Rawalpindi than the long-term stability and coherence of the Pakistani state itself. Stephen P. Cohen, the Brookings Institution scholar, says that if Pakistan were not in possession of nuclear weapons, the problem would not be nearly the same. Pakistan without nuclear weapons, he says, would be the equivalent of “Nigeria without oil”—a much lower foreign-policy priority.

American strategists like Cohen argue that the U.S. must maintain its association with a nuclear Pakistan over the long term for three main reasons. The first is that an unstable and friendless Pakistan would be more apt to take precipitous action against India; the second is that nuclear material, or a warhead, could go missing; the third, longer-term worry is that the Pakistani state itself could implode. “One of the negative changes we’ve seen is that Pakistan is losing its coherence as a state,” Cohen said. “Its economy has failed, its politics have failed, and its army either fails or looks the other way. There are no good options.” Few experts believe that Pakistan is in imminent danger of complete collapse—but the trends, as Cohen notes, are wholly negative. The government is widely considered to be among the world’s most corrupt. (President Asif Ali Zardari is himself informally known as “Mr. 10 Percent.”) Last year, Pakistan’s inflation rate hit a high of 15 percent, and the real unemployment rate was 34 percent. Some 60 percent of Pakistanis survive on less than $2 a day. Nearly a quarter of the government budget goes to the military.

In a country that has achieved only modestly in the realms of innovation, science, and education (especially in comparison with its rival, India), the Pakistani nuclear program has played an outsized role in the building of national self-esteem. And so criticism of the program is deeply wounding, and produces feelings of paranoia.

In 2000, one of the authors of this article met A. Q. Khan, the nuclear scientist known as the “father” of Pakistan’s nuclear-bomb program, at a ceremony in Islamabad meant to mark the second anniversary of the detonation of the country’s first atomic bomb. (Khan was also the principal exporter of Pakistani nuclear technology to such countries as Iran, North Korea, and Libya.) The celebration—complete with a vanilla sheet cake on which the words Youm-e-Takbeer, or “Day of God’s Greatness,” were written in lemon frosting—was held in the presence of many of the country’s leading nuclear scientists, and of General Musharraf, who had recently come to power in a coup. After the ceremony, Khan told a small circle of admiring nuclear scientists, as well as the visiting American reporter, that the U.S. and the rest of the West resented Pakistan’s admission into the nuclear club. “The West has been leading a crusade against the Muslims for a thousand years,” he said. He went on to assert that the U.S. would do anything in its power to neutralize Pakistan’s nuclear assets. One of the scientists in the circle agreed, and said, “Why do the Americans want to destroy Islam?”

This sort of paranoia has spread through the Pakistani security elite—and it went viral after the Abbottabad raid. Fear of pernicious American designs on Pakistan’s nuclear arsenal has combined with people’s anger over their military’s apparent impotence, creating a feeling of almost toxic insecurity across the country. The raid shook the confidence of the army, and its admirers, like no other event since Pakistan’s most recent defeat by the Indian army, in 1999. (There have been multiple wars between India and Pakistan, all of them won by India.) When U.S. Navy SEALs penetrated Pakistani air defenses, landed in helicopters streets away from a prestigious military academy, killed the most-wanted fugitive in modern history, and then departed, the Pakistani military was oblivious for the duration. Pervasive derision followed. A popular text message in the days after the raid read, “If you honk your horn, do so lightly, because the Pakistani army is asleep.”

A retired Pakistani general, who expressed disgust at the military’s performance (“There should have been a try to shoot down the American helicopters”), says that the raid intensified traditional Pakistani insecurities. “You can think of this in terms of drones. The Americans are in the skies, where they are invisible, and yet they can kill anyone they want. America is a superpower of technology. It would be easy to make a quick snatch of Pakistani strategic assets.”

Pakistanis tend to believe that America seeks to seize their country’s nuclear weapons preemptively, simply because the U.S. doesn’t like their country, or because of a preexisting ideological commitment to keep Muslim countries nuclear-free. This paranoia is not completely irrational, of course; it’s wise for the U.S. to try to design a plan for seizing Pakistan’s nuclear weapons in a low-risk manner. “The U.S. tried to prevent Pakistan from becoming a nuclear-weapons state,” said Graham Allison of Harvard’s Belfer Center. “It is not delusional for Pakistan to fear that America is interested in de-nuking them. It is prudent paranoia.”

Supporters of an Islamic separatist group march a mock nuclear missile through the streets of Karachi, February 2011. (Reuters)

Though the U.S. has punished Pakistan in the past for its nuclear program (with sanctions that not only failed to stop the program, but helped to aggravate anti-American feeling among Pakistanis), there is no evidence to suggest that any official of the Obama administration is actively considering “de-nuking” Pakistan in its current state. Officials at the White House and elsewhere argue that the Pakistani military and the SPD are the best tools available to keep Pakistan’s weapons secure. In the recent past, the U.S. has spent as much as $100 million to help the SPD build better facilities and safety-and-security systems. (However, according to David Sanger in his book, The Inheritance, Pakistan has not allowed the U.S. to conduct an audit to see how the $100 million was spent.) One area where Admiral Mullen felt his relationship with General Kayani had borne fruit was over nuclear weapons. “When he would bring up a concern about nuclear weapons in a meeting, the Pakistanis would usually deal with it,” an associate of Mullen’s told us.

But Pakistanis are correct to believe that the U.S. government—because it does not trust Pakistan, because it knows that the civilian leadership is weak, and because it does not have a complete intelligence picture—is worried that the SPD could fail in its mission, and that fissile material or a nuclear weapon could go missing. Pakistanis are also correct to believe that the Pentagon—concerned that Pakistan, beset by ethnic division, corruption, and dire levels of terrorism, could one day come apart completely—has developed a set of highly detailed plans to grapple with nuclear insecurity in Pakistan. “It’s safe to assume that planning for the worst-case scenario regarding Pakistan nukes has already taken place inside the U.S. government,” Roger Cressey, a former deputy director of counterterrorism under Bill Clinton and George W. Bush, told NBC News in August. “This issue remains one of the highest priorities of the U.S. intelligence community … and the White House.” From time to time, American officials have hinted publicly that there are concrete plans in place in the event of a Pakistani nuclear emergency. For instance, during Senate hearings for her confirmation as secretary of state in 2005, Condoleezza Rice, who was then President Bush’s national-security adviser, was asked by Senator John Kerry what would happen to Pakistan’s nukes in the event of an Islamic coup in Islamabad. “We have noted this problem, and we are prepared to try to deal with it,” Rice said.

Those preparations have been extensive. According to military and intelligence sources, any response to a Pakistani nuclear crisis would involve something along the following lines: If a single weapon or a small amount of nuclear material were to go missing, the response would be small and contained—Abbottabad redux, although with a higher potential for U.S. casualties. The United States Joint Special Operations Command (JSOC) maintains rotating deployments of specially trained units in the region, most of them Navy SEALs and Army explosive-ordnance-disposal specialists, who are trained to deal with nuclear weapons that have fallen into the wrong hands. Their area of operation includes the former Soviet states, where there is a large amount of loose fissile material, and, of course, Pakistan. JSOC “has units and aircraft and parachutes on alert in the region for nuclear issues, and regularly inserts units and equipment for prep,” says a military official who was involved in supporting these technicians. Seizing or remotely disabling a weapon of mass destruction is what’s known in military jargon as a “render-safe mission”—and render-safe missions have evidently been successfully pulled off by JSOC in the past. In his memoir, Hugh Shelton, who chaired the Joint Chiefs of Staff from 1997 to 2001, recalls an incident from the 1990s in which the CIA told the Special Operations Command that a ship had left North Korea with what Shelton describes as “an illegal weapon” on board. Where it was headed, the U.S. didn’t know. He wrote:

It was a very time-sensitive mission in which a specific SEAL Team Six component was called into action. While I cannot get into the tactical elements or operational details of this mission, what I can say is that our guys were able to “immobilize” the weapon system in a special way without leaving any trace.

Much more challenging than capturing and disabling a loose nuke or two, however, would be seizing control of—or at least disabling—the entire Pakistani nuclear arsenal in the event of a jihadist coup, civil war, or other catastrophic event. This “disablement campaign,” as one former senior Special Operations planner calls it, would be the most taxing, most dangerous of any special mission that JSOC could find itself tasked with—orders of magnitude more difficult and expansive than Abbottabad. The scale of such an operation would be too large for U.S. Special Operations components alone, so an across-the-board disablement campaign would be led by U.S. Central Command—the area command that is responsible for the Middle East and Central Asia, and runs operations in Afghanistan and Iraq—and U.S. Pacific Command.

JSOC would take the lead, however, accompanied by civilian experts, and has been training for such an operation for years. JSOC forces are trained to breach the inner perimeters of nuclear installations, and then to find, secure, evacuate—or, if that’s not possible, to “render safe”—any live weapons. At the Nevada National Security Site, northwest of Las Vegas, Delta Force and SEAL Team Six squadrons practice “Deep Underground Shelter” penetrations, using extremely sensitive radiological detection devices that can pick up trace amounts of nuclear material and help Special Operations locate the precise spot where the fissile material is stored. JSOC has also built mock Pashtun villages, complete with hidden mock nuclear-storage depots, at a training facility on the East Coast, so SEALs and Delta Force operatives can practice there.

At the same time American military and intelligence forces have been training in the U.S for such a disablement campaign, they have also been quietly pre-positioning the necessary equipment in the region. In the event of a coup, U.S. forces would rush into the country, crossing borders, rappelling down from helicopters, and parachuting out of airplanes, so they could begin securing known or suspected nuclear-storage sites. According to the former senior Special Operations planner, JSOC units’ first tasks might be to disable tactical nuclear weapons—because those are more easily mated, and easier to move around, than long-range missiles.

In a larger disablement campaign, the U.S. would likely mobilize the Army’s 20th Support Command, whose Nuclear Disablement Teams would accompany Special Operations detachments or Marine companies into the country. These teams are trained to engage in what the military delicately calls “sensitive site exploitation operations on nuclear sites”—meaning that they can destroy a nuclear weapon without setting it off. Generally, a mated nuclear warhead can be deactivated when its trigger mechanism is disabled—and so both the Army teams and JSOC units train extensively on the types of trigger mechanisms that Pakistani weapons are thought to use. According to some scenarios developed by American war planners, after as many weapons as possible were disabled and as much fissile material as possible was secured, U.S. troops would evacuate quickly—because the final stage of the plan involves precision missile strikes on nuclear bunkers, using special “hard and deeply buried target” munitions.

But nuclear experts issue a cautionary note: it is not clear that American intelligence can identify the locations of all of Pakistan’s nuclear weapons, particularly after the Abbottabad raid. “Anyone who tells you that they know where all of Pakistan’s nukes are is lying to you,” General James Jones, President Obama’s first national-security adviser, has said, according to a source who heard him say it. (When asked by the authors of this article about his statement, General Jones issued a “no comment.”) Another American former official with nuclear expertise says, “We don’t even know, on any given day, exactly how many weapons they have. We can get within plus or minus 10, but that’s about it.”

Pakistan’s military chiefs are aware that America’s military has developed plans for an emergency nuclear-disablement operation in their country, and they have periodically threatened to ally themselves with China, as a way to undercut U.S. power in South Asia. In a recent statement quite obviously meant for American ears, Pakistan’s prime minister, Yousuf Raza Gilani, described the Pakistani-Chinese relationship as “higher than the mountains, deeper than the oceans, stronger than steel, and sweeter than honey.” But China, too, is worried about Pakistan’s stability, and has recently alleged that Pakistan has harbored Uighur separatists operating in western China. According to American sources, China has, in secret talks with the U.S., reached an understanding that, should America decide to send forces into Pakistan to secure its nuclear weapons, China would raise no objections. (An Obama-administration spokesperson had no comment.)

The U.S. takes great pains to stress to the Pakistanis that any disablement or render-safe plans would be put into effect only in the event that everything else fails—and furthermore, that these plans have the primary goal of helping to maintain Pakistan’s secure possession of the weapons over the long term. (In fact, some Pakistani officials accept these American plans—they welcome American technical and military assistance in keeping nuclear material out of the wrong hands.) Still, the subject comes up at almost every high-level meeting between U.S. and Pakistani officials.

According to U.S. military planners, preparations for the emergency denuclearization of Pakistan are on par with only two other priority-one global-crisis plans: one involves the possible U.S. invasion of Iran and the other involves a possible conflict with China. All three of these potential crises are considered low-probability but high-risk, to be prepared for accordingly.

Another plausible nuclear scenario is that India and Pakistan will once again go to war, with potentially cataclysmic consequences. One scenario advanced frequently by analysts sees Pakistan and India descending into armed confrontation after another Mumbai-style attack launched by the allegedly ISI-affiliated Lashkar-e-Taiba, or by another of the jihadist groups given shelter and aid in Pakistan. India, in a feat of forbearance, did not respond militarily to the November 2008 attacks, but its defense minister warned in June: “If a provocation is to happen again, I think it would be hard to justify to our people such a self-restraint.”

If an attack should happen, it might not necessarily be prompted by a specific ISI order. Lashkar-e-Taiba, like other groups supported and protected by the Pakistani government, does not have a perfect record of complying with ISI instructions, according to a Pakistani source familiar with the relationship. Even though Lashkar cells maintain contact with ISI officers, they operate according to their own desires and schedules. “The ISI funds them and protects them, but doesn’t always control their choice of targets and timing,” the Pakistani source says.

David Albright, a physicist and the president of the Institute for Science and International Security, imagines the scenario this way: “India responds to an act of terrorism with a conventional attack inside Pakistan, on the base of the group that committed the act, and it escalates from there. India could target the facilities of the Pakistani nuclear-weapons program, and then you have the real risk of escalation, because of Pakistani paranoia that India is trying to take away its nuclear arsenal.”

Experts worry about the accidental launch of a nuclear warhead during a period of high tension between Pakistan and India, or that rogue elements inside the Pakistani military will take it upon themselves to initiate a nuclear attack. On paper, Pakistan’s nuclear command-and-control body, the National Command Authority, is overseen by the civilian prime minister, working in conjunction with the country’s military leaders—but the military controls the system of enabling and authenticating codes that would be transmitted to strategic forces in the event of a nuclear alert. Pakistan’s nuclear posture is opaque, however, and the U.S. has many questions about how the authority to use the weapons is delegated.

In 2006, General Kidwai, the SPD leader, told a U.S. audience at the Naval Postgraduate School in Monterey, California, that Pakistan maintained for its nuclear arsenal the functional equivalent of two-person control and permissive action links, or PALs—coded locks meant to prevent unauthorized arming of a weapon. When asked about Pakistan’s PAL protocols, one former U.S. defense official replied, “It has never been clear to me what Pakistani PALs really entail. The doctrine is ‘two people’—but is it two people to unlock the box around the warhead, or is it two people to launch the thing once you’ve mated the warhead to the missile?” (India, in contrast, has been more transparent about its nuclear posture; unlike Pakistan, it has pledged not to use nuclear weapons first—only in response.)

The policy goals of the Obama administration are focused not on Pakistan’s nuclear program, but rather on the terrorist groups based there. “Our core goal is to disrupt, dismantle, and eventually defeat al-Qaeda,” one senior administration official says. “This is a very clarifying way to think about what we are doing and why cooperation with Pakistan is important.”

This narrow focus has led to some achievements—not only the bin Laden raid, which was obviously accomplished without the cooperation of the ISI, but also the capture or killing (with the ISI’s help) of several other al-Qaeda figures over the years. This focus on al-Qaeda may have sidelined other tactical priorities (such as trying to disrupt and defeat Pakistani groups providing assistance to the Afghan Taliban) and has led to some uncomfortable trade-offs. When asked why the U.S. doesn’t target the factories located on Pakistani territory that produce the improvised explosive devices deployed by the Taliban against American troops inside Afghanistan, the same senior Obama-administration official said: “What we want to do, above all else, is not lose progress on the core goal” of defeating al-Qaeda, a goal that calls for continuing to cooperate with, and to fund, the ISI. So: the U.S. funds the ISI; the ISI funds the Haqqani network; and the Haqqani network kills American soldiers.

Another senior administration official, when presented with this formula, said: “It’s not as simple as that. We’ve identified a core interest, and we wouldn’t have been able to make as much progress as we’ve made, without Pakistan. A lot of the assistance we provide them is focused on specific counterterrorism issues. This is not just cutting a check.” Money, of course, is fungible—funds earmarked for fighting al-Qaeda can end up supporting the Haqqani network, which is fighting the United States. But, the senior official said, “we have demonstrated that we will impose restrictions on assistance, and withhold assistance for a time, if the Pakistanis aren’t cooperating with us”—a reference to a recent decision by the administration to temporarily hold back $800 million in reimbursements for counterterror activities and other military aid.

To Stephen P. Cohen, the Pakistan analyst at Brookings, the administration’s singular focus on al-Qaeda means that American policy makers are not focused on larger issues. The rationale for continued, even heightened, engagement with Pakistan, he said, is that the country is “too nuclear to fail.” The arguments made by the administration about the importance of focusing on al-Qaeda at the expense of focusing on Pakistan per se remind Cohen of arguments from the Cold War. “It’s the same line I heard 20 years ago in the State Department,” he says. “The program was to get the Soviets out of Afghanistan. We privileged one goal over another. In Pakistan we have several goals, but we are ignoring the Pakistani nuclear-weapons program, ignoring India-Pakistan relations, ignoring the country’s growing societal degradation. We have to have a better policy than keeping our fingers crossed.”

Few policy makers believe that cutting aid to Islamabad is practical, especially while American troops in Afghanistan depend on supplies trucked through Pakistan. Even Admiral Mullen, who has been disillusioned by the behavior of Pakistan’s ruling generals, argued before the Senate Armed Services Committee just prior to his retirement that the U.S. must not give up on its relationship with Pakistan. “Now is not the time to disengage from Pakistan; we must, instead, reframe our relationship,” he said. “A flawed and strained engagement with Pakistan is better than disengagement.”

Influential lawmakers have argued that the U.S. should not hesitate to strike at targets inside Pakistan that threaten American interests. American drones, of course, operate in the skies over Pakistan’s northern tribal areas, but these missions are generally conducted against jihadists who have also turned against the Pakistani government. But some lawmakers, such as Lindsey Graham, the senior Republican senator from South Carolina, suggest that the U.S. take a more unilateral approach to its own defense. “The sovereign nation of Pakistan is engaging in hostile acts against the United States, and our ally Afghanistan, that must cease,” Graham recently told Fox News Sunday. “If the experts believe that we need to elevate our response, they will have a lot of bipartisan support on Capitol Hill.”

Talk like this has apparently concentrated the attention of Pakistan’s military leaders, as it has in the past: recall that the Pakistanis fired an ISI chief after the administration of President George H. W. Bush threatened to place Pakistan on the list of state sponsors of terror. But this sort of rhetoric must be accompanied by efforts to heighten U.S. engagement. On one level, it is perverse to speak of expanding a relationship with a country so obviously working against so many U.S. interests. But a new, revamped policy is obviously needed—an honest one, as Admiral Mullen has indicated, in which strategic differences are ventilated rather than papered over, and in which the U.S. broadens its engagement with all sectors of Pakistani society. There is very little that agitates Pakistani leaders more than the feeling that the United States is being disrespectful to their country—particularly in failing to acknowledge the thousands of Pakistani victims killed by militants during the war on terror. The “riot act” should no longer be read, or at least not read publicly. Americans have been reading the riot act to the Pakistanis for at least 20 years over the issue of terrorism, and it hasn’t worked. This should motivate American policy makers to devise a new approach, while remaining focused on the most important goal: keeping Pakistan’s nuclear arsenal secure and holstered.

“South Asia remains the most dangerous nuclear-confrontation zone in the world, and these are not issues we can solve unilaterally,” says Toby Dalton, the deputy director of the Nuclear Policy Program at the Carnegie Endowment for International Peace and a former Department of Energy representative at the U.S. Embassy in Islamabad. “We share a common goal with Pakistan, in preventing nuclear war and preventing terrorists from gaining access to a nuclear weapon. We have to work with them on nuclear security and have meaningful technical exchanges on best practices. This has to continue.”

The United States must, for its own security, keep watch over Pakistan’s nuclear program—and that’s more easily done if we remain engaged with the Pakistani government. The U.S. must also be able to receive information from the ISI about al-Qaeda, even if such information is provided sporadically. And the U.S. will simply not find a way out of Afghanistan if Pakistan becomes an open enemy. Pakistan, for its part, can afford to lose neither America’s direct financial support, nor the help America provides with international lending agencies. Nor can Pakistan’s military afford to lose its access to American weapons systems, and to the trainers attached to them. Economically, Pakistan cannot afford to be isolated by America in the way the U.S. isolates countries it considers sponsors of terrorism. Its neighbor Iran is an object lesson in this regard. For all these reasons, Pakistan and America remain locked in a hostile embrace.

There is no escaping this vexed relationship—and little evidence to suggest that it will soon improve. But the American officials in closest contact with the Pakistanis—Admiral Mullen being the notable exception—still seem predisposed to optimism, apparently embracing the belief that Islamabad will change through tough love. A senior U.S. intelligence official told us that General David Petraeus, the new director of the CIA, says he believes he can rebuild relations with the ISI, because he has “a good personal relationship with these guys.”