In May 2010, in the aftermath of the attempted bombing of Times Square by a jihadist with ties to the Pakistani Taliban, Secretary of State Hillary Clinton gave an interview to 60 Minutes and made a startling claim about the government in Pakistan. “I’m not saying that they’re at the highest levels, but I believe that somewhere in this government are people who know where Osama bin Laden and al Qaeda is, where Mullah Omar and the leadership of the Afghan Taliban is, and we expect more cooperation to help us bring to justice, capture or kill, those who attacked us on 9/11.”

Why would Clinton say this? Did the U.S. government have intelligence—an inside source, communications intercepts—that Pakistani officials knew where bin Laden was hiding? Or was America’s top diplomat just engaging in idle speculation about a nation often described as a key ally in the war on terror?

One hint: She had made similar comments before.

A year later, two days after a team of Navy SEALs had killed bin Laden at his compound in Abbottabad, CIA director Leon Panetta was even more blunt. In an interview with Time magazine’s Massimo Calabresi, Panetta explained why the United States went in on its own: “It was decided that any effort to work with the Pakistanis could jeopardize the mission. They might alert the targets.”

That is a stunning statement. If Clinton would not accuse officials at the “highest levels” of the Pakistani government of al Qaeda sympathies, Panetta did. The CIA director does not deal with anyone other than officials at the highest levels of partner governments. So Panetta wouldn’t withhold information simply out of concern that there are al Qaeda sympathizers or agents seeded among the midlevel ranks of Pakistan’s military and ISI intelligence agency. He was concerned that the leaders of these institutions might alert the targets.

It was a reasonable concern for two reasons: the surprising location of bin Laden’s compound and the long history of support for jihadists from within the Pakistani security apparatus.

In August 2010, the U.S. intelligence community tracked Abu Ahmed al-Kuwaiti, a courier known to be very close to bin Laden, to a large compound in Abbottabad, just 40 miles from Islamabad, Pakistan’s capital city. The one-acre property immediately stood out. It was eight times larger than most of the surrounding lots, and it was contained by high walls topped with barbed wire—some rising to more than 15 feet. There were no obvious telephone or cable lines. From a nearby safe house, the CIA monitored the activities of the residents. Among other oddities, they burned their garbage rather than put it out for collection. A seven-foot wall on the third floor was high enough to allow a tall man to get some fresh air without being seen by his neighbors. But even after the intelligence community concluded that bin Laden was probably living there—a 60-80 percent likelihood, the CIA estimated—the location raised doubts.

Abbottabad is home to the Kakul Military Academy, often described as Pakistan’s West Point. As a result, many military officials retire there, to be close to their friends from the army. It frequently hosts high-ranking military officers and visiting foreign dignitaries. A week before the U.S. assault on bin Laden’s compound, the head of Pakistan’s military, General Ashfaq Parvez Kayani, spoke at a ceremony on the grounds of the academy. In February 2010, General David Petraeus paid a visit to Kakul.

So as CIA analysts learned everything they could about the property, one question kept coming up: Is it possible that the world’s most wanted man is hiding in the shadows of one of Pakistan’s best-known military garrisons without the knowledge of that country’s top officials? They looked—and listened—for signs that official Pakistan was helping those ensconced in the compound. They did not find any.

Still, as Panetta’s comment suggests, the absence of that evidence did not allay suspicions that high-ranking Pakistani officials were aware of bin Laden’s presence. And no wonder.

Bin Laden’s links to Pakistan dated to the 1980s, when he was a liaison between Saudi intelligence, Pakistani intelligence, and the so-called Arab Afghans who traveled from the Middle East to fight the Soviets. While the war against the Soviets was fought in Afghanistan, the Arab Afghan network bin Laden led was based in Pakistan.

Al Qaeda was headquartered for several years in Sudan in the 1990s, during which time bin Laden refashioned the Arab Afghan network into an international terrorist network. But after the Sudanese government expelled the terror master, al Qaeda relocated to Afghanistan, almost certainly with the help of Pakistan’s Inter-Services Intelligence—the ISI.

According to the 9/11 Commission: “It is unlikely that bin Laden could have returned to Afghanistan had Pakistan disapproved. The Pakistani military intelligence service probably had advance knowledge of his coming, and its officers may have facilitated his travel.” During his time away from South Asia, bin Laden had “maintained guesthouses and training camps in Pakistan and Afghanistan.” But he would have needed to broker a deal with the new power inside Afghanistan, Mullah Omar, in order to resettle there.

The ISI made that happen. “Pakistani intelligence officers reportedly introduced bin Laden to Taliban leaders in Kandahar, their main base of power, to aid his reassertion of control over camps near Khowst, out of an apparent hope that he would now expand the camps and make them available for training [Pakistan-backed] Kashmiri militants,” reported the 9/11 Commission.

The value of Pakistan’s assistance to bin Laden at this time cannot be overestimated. After being expelled from Sudan, the 9/11 Commission found, bin Laden “was in his weakest position since his early days in the war against the Soviet Union.” He was desperate for a new ally who would host his network and allow him to rebuild. Mullah Omar’s Taliban, an ISI proxy, gave him just that.

Newly ensconced in Afghanistan, bin Laden rebuilt al Qaeda quickly and within just a few years showed off his group’s deadly capabilities. On August 7, 1998, al Qaeda launched simultaneous suicide truck bomb attacks on the U.S. embassies in Kenya and Tanzania. It was al Qaeda’s most successful operation prior to 9/11, killing hundreds. In the wake of the attacks, President Clinton authorized missile strikes against a suspicious factory in Sudan and bin Laden’s training camps in Afghanistan.

From a tactical perspective, the strikes mostly failed. A few dozen al Qaeda trainees and operatives were killed, but bin Laden escaped. Several Clinton administration officials and intelligence officers thought they knew why. “Officials in Washington speculated that one or another Pakistani official might have sent a warning to the Taliban or bin Laden.” Adding to their suspicions was the fact that several Pakistani military intelligence officials were among the dead at one of bin Laden’s camps.

In early 1999, Clinton officials were still exploring ways to get bin Laden. The main obstacle, they feared, was Pakistan. National Security Adviser Sandy Berger “suggested sending one U-2 flight” over Afghanistan in an effort to locate bin Laden. The spy plane would have to fly over Pakistani airspace; Clinton’s chief counterterrorism adviser, Richard Clarke, objected on the grounds that Pakistani intelligence “is in bed with” bin Laden and would warn him. “Armed with that knowledge, old wily Usama will likely boogie to Baghdad,” Clarke warned. (Clinton administration officials had received multiple intelligence reports saying that Saddam Hussein wanted bin Laden in Baghdad at the time.)

The 9/11 attacks ushered in a new era of American-Pakistani cooperation against al Qaeda. But the alliance was not a natural one—nor did it come about easily. Pakistan had built Mullah Omar’s Taliban to wage a proxy war in Afghanistan. After al Qaeda executed the most devastating terrorist attack in history, Omar refused to disavow al Qaeda’s leader. Pakistan’s ally in Afghanistan was now one of America’s chief enemies.

The deployment of American-led forces to the region and rapid overthrow of the Taliban undoubtedly influenced Pakistani behavior. In his memoir, former President Pervez Musharraf says that Deputy Secretary of State Richard Armitage threatened to bomb Pakistan “back to the Stone Age” if Musharraf’s regime did not cooperate. (Armitage denies he made such a threat, but the tough U.S. position vis-à-vis Pakistan is not in question.)

So deep were the ties between Islamabad and the Taliban that Musharraf was initially undecided about abandoning his erstwhile ally. Musharraf claims that he “war-gamed the United States as an adversary” and concluded, in a “dispassionate, military-style analysis,” that the costs of defying Washington outweighed the benefits.

Musharraf’s account may be a self-serving fiction intended to prop up his image as an independent-minded leader who only had Pakistan’s interests at heart. Even so, it is telling that he would express his misgivings about allying with the United States in such a way. “The ultimate question that confronted me was whether it was in our national interest to destroy ourselves for the Taliban,” Musharraf writes. “Were they worth committing suicide over? The answer was a resounding no.”

In reality, however, the answer to Musharraf’s question was not so straightforward. Whether motivated by an American threat or the billions of dollars it received in U.S. aid, Pakistan did offer vital assistance in the immediate aftermath of 9/11. Hundreds of Taliban and al Qaeda members were captured in late 2001 as they attempted to flee Afghanistan’s Tora Bora mountains for the unsettled areas of northern Pakistan. Many of them were transferred to American custody and detained at Guantánamo Bay.

Pakistan also helped American counterterrorism officials hunt down important al Qaeda operatives who were plotting more attacks on U.S. soil from their hideouts in Pakistan’s cities. Senior al Qaeda operative Abu Zubaydah, 9/11 point man Ramzi bin al-Shibh, and 9/11 mastermind Khalid Sheikh Mohammed (KSM) are the most noteworthy captures from 2002 and 2003. And the counterterrorism cooperation continued in the years that followed. In 2005, for example, Pakistani authorities captured Abu Faraj al Libi, KSM’s replacement as al Qaeda’s external operations chief. Press reports indicate that the CIA’s interrogations of KSM and al Libi played a role in identifying the courier who ultimately led a Navy SEAL team to bin Laden’s door.

Even while providing crucial assistance in the fight against al Qaeda, Pakistan kept the Taliban alive. Mullah Omar relocated to Quetta, and his Pakistani protection became so obvious that his new leadership council came to be called the Quetta Shura Taliban (QST). Gulbuddin Hekmatyar, an old ISI client from the days of jihad against the Soviets, reestablished his base of operations in northern Pakistan. The same is true for the father and son team of Jalaluddin and Siraj Haqqani, who were also longtime clients of the ISI.

These three organizations—the QST, Gulbuddin’s Hezb-i-Islami, and the Haqqani network—are the principal insurgency groups in Afghanistan today. The Pakistani military-intelligence establishment has actively aided and abetted them. These three groups have something else in common: They are closely allied with Osama bin Laden’s al Qaeda. Siraj Haqqani, who now leads his father’s network, sits on al Qaeda’s elite Shura council and may have a say in who replaces bin Laden as al Qaeda’s top man. Hekmatyar was one of bin Laden’s friends from the 1980s. To this day, al Qaeda fights alongside these ISI-backed organizations against the United States and its allies in Afghanistan.

In 2008, Lieutenant Colonel Chris Nash, an American commander who advised the Afghan border police, told the Army Times that the ISI “flew repeated helicopter missions into Afghanistan to resupply the Taliban during a fierce battle in June 2007.” A copy of a presentation authored by Nash reads: “ISI involved in direct support to many enemy operations. .  .  . Classification prevents further discussion of this point.” The ISI support included “training, funding, [and] logistics” to the Taliban and allied insurgency groups.

In July 2008, the ISI was caught red-handed aiding U.S. enemies when the Haqqani network bombed the Indian embassy in Kabul. The Indian defense attaché and more than 50 others were killed. The following month the New York Times reported that American officials had confronted the Pakistanis with evidence of their complicity, including “intercepted communications between Pakistani intelligence officers and militants who carried out the attack.” Remarkably, the Times also reported that the ISI was warning Taliban and al Qaeda terrorists about U.S. drone attacks: “American officials also said there was new information showing that members of the Pakistani intelligence service were increasingly providing militants with details about the American campaign against them, in some cases allowing militants to avoid American missile strikes in Pakistan’s tribal areas.”

That collaboration continues. In late April, Obama dispatched his top military officer to Islamabad in an effort to repair the rapidly deteriorating relationship between the United States and Pakistan. In a series of high-level meetings, Admiral Mike Mullen, chairman of the Joint Chiefs of Staff, sought to renew the military and intelligence partnerships between the two countries. In his public remarks, Mullen had praise for the civilian government and the efforts of Pakistan’s security services to help in the battle against jihadists. “Throughout the visit, the admiral emphasized the long-term U.S. commitment to supporting Pakistan in its fight against violent extremists,” read a statement issued by the U.S. embassy.

But in an interview with one of Pakistan’s most widely read newspapers, the Dawn, Mullen offered an assessment that contrasted dramatically with the happy talk. “It’s fairly well known that ISI has a long-standing relationship with the Haqqani network,” he said. “Haqqani is supporting, funding, training fighters that are killing Americans and killing coalition partners. And I have a sacred obligation to do all I can to make sure that doesn’t happen. So that’s at the core—it’s not the only thing—but that’s at the core that I think is the most difficult part of the relationship.”

Recently leaked files produced at Guantánamo provide more examples of Pakistan’s duplicity. One leaked Gitmo file contains a “list of terrorist and terrorist support entities” associated with al Qaeda and the Taliban. The U.S. officials who authored the document wrote: “Through associations with these groups and organizations, a detainee may have provided support to al Qaeda or the Taliban, or engaged in hostilities against U.S. or Coalition forces.” Even though Pakistan helped capture many of the detainees who have been held at Guantánamo, Pakistan’s ISI intelligence agency is included on the list.

Another leaked Gitmo file contains a striking example of Pakistan’s dual loyalties in the war on terror. The file notes that in January 2003, “Three Pakistani military officers provided .  .  . training .  .  . in explosives, bomb-making, and assassination techniques” to a group of Taliban commanders. “This training was conducted in preparation for a planned spring campaign to assassinate Westerners.” A few months later, members of this same Taliban group kidnapped and killed an International Red Cross worker in Afghanistan.

The Afghan insurgency groups are not the only Pakistan-backed terrorist organizations to maintain close ties to al Qaeda. After news of bin Laden’s death was made public, Laskhar-e-Taiba’s founder, Hafiz Muhammad Saeed, put out a statement through his spokesman. “Osama bin Laden was a great person who awakened the Muslim world,” Saeed was quoted by Reuters as saying. “Osama bin Laden has rendered great sacrifices for Islam and Muslims, and these will always be remembered.”

Lashkar-e-Taiba (LeT) was founded in the 1990s with assistance from both the ISI and bin Laden to fight Indian forces in Kashmir. It has since evolved into an organization with an international reach. The U.S. government has put considerable pressure on the Pakistani government to crack down on the LeT—to no avail. The LeT operates openly in Pakistan, sometimes under an assumed name. The LeT’s most notorious attack came in November 2008, when well-trained gunmen laid siege to Mumbai. More than 160 people were killed, with hundreds more wounded.

The operation showed the degree to which al Qaeda’s ideology had been adopted by Pakistan’s indigenous terrorist groups. After the attack, Indian officials released transcripts of intercepted telephone calls between the Mumbai attackers and individuals connected to the Pakistani military-intelligence establishment. Indian and American authorities both linked a Pakistani-American named David Headley to the attack. Headley, formerly known as Daood Sayed Gilani, was convinced by the LeT to change his name so that his international travels would avoid scrutiny. He performed surveillance on the LeT’s targets in Mumbai and reportedly confessed to the ISI’s involvement in the assault.

The FBI concluded that Headley had reported to a former Pakistani military officer named Ilyas Kashmiri. As the operational commander of Harkat-ul-Jihad-al-Is-lami (HUJI), another Pakistani-based terrorist group with historical ties to the ISI, Kashmiri developed close ties to al Qaeda. In 2010, the U.S. Treasury Department designated Kashmiri as a terrorist, saying in a statement that he “is responsible for creating a cadre of militants to act on behalf of HUJI and al Qaeda.”

The reality is that al Qaeda has developed close ties to virtually all of the Pakistani terrorist organizations that have been used as proxies by the ISI. These same organizations provide a deep bench for al Qaeda to use when replacing fallen leaders. Another of these organizations is Jaish-e-Mohammad (JeM). Like the LeT, JeM was created with assistance from the ISI to wage jihad against India in Kashmir but has evolved into an international jihadist organization. JeM terrorist Rashid Rauf, for example, became a top operational leader within al Qaeda. Rauf has been tied to al Qaeda’s 2006 plot against U.K.-based -airliners, among other attacks.

The jihadist violence unleashed by the Pakistani military and intelligence establishment has engulfed Pakistan itself. Suicide bombings have become commonplace. And this violence has been directed at the very organs of the Pakistani state that helped cause it. The Pakistani Taliban (Tehrik-i-Taliban Pakistan), an organization that is strongly affiliated with al Qaeda, has targeted ISI and military targets. Led by Hakimullah Mehsud, an ally of bin Laden, the TTP was also responsible for the failed attack on Times Square in May 2010.

In interviews since Osama bin Laden was killed, officials from across the U.S. government have refused to accuse their Pakistani counterparts of complicity in the hiding of the al Qaeda mastermind. But suspicions run deep.

“My best assessment is that their behavior is such that they are surprised by what we found,” says a senior administration official. “But I am not in a position to give them a clean bill of health at this point.”

“I can say with high confidence that those at the top of the Pakistani military and its intelligence service did not know where bin Laden was hiding,” says one official with direct knowledge of the intelligence.

Others warn that such assessments must be parsed literally. The handful of individuals at the very top of those institutions are provisionally beyond suspicion, in other words. But how do we know? No one currently serving would say. One strong possibility: The U.S. government was monitoring their reactions in real time, listening as the assault on bin Laden’s compound went down.

We will soon know more. Document exploitation teams are analyzing the surprising amount of information taken from bin Laden’s compound during the raid. Among their chief objectives: determining what role, if any, top Pakistani government officials played in harboring the fugitive Osama bin Laden over the last decade of his life.

Stephen F. Hayes is a senior writer at The Weekly Standard. Thomas Joscelyn is a senior fellow at the Foundation for Defense of Democracies.

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