The New Republic

In the stash of hard drives, thumb drives, and personal papers discovered in Osama bin Laden’s compound, one especially revealing find was his personal diary. According to an analyst privy to the frequent updates of translated material being posted to the intelligence community’s classified internet, the late Al Qaeda leader periodically recorded his amusement that U.S. drones were searching for him in the mountainous border region between Afghanistan and Pakistan while he was living comfortably less than a quarter of a mile from a Pakistani military academy. “Bin Laden was yukking it up about how clueless we were,” the source says.

The joke ended up being on bin Laden, but it’s worth asking why he felt so cocky. He was, after all, the world’s most wanted man, and yet there were only a few bodyguards at his compound. Did bin Laden believe he would be tipped off before a SEAL team knocked down his door?

To survive for six years in the posh Islamabad suburb of Abbottabad, bin Laden almost certainly relied on what might be called a “deep state”—a network of current and retired intelligence and military officers who are actively undermining the official policy of Pakistan’s government. “I have no doubt that members of Pakistan’s military and intelligence services knew of bin Laden’s whereabouts,” says Representative Steve Rothman, a New Jersey Democrat who sits on the House subcommittees that fund the military and foreign-aid budgets and who has attended top-secret briefings on the May 1 raid. “The question remains, however, how far that knowledge went up the command chain in Pakistan.”

All modern democratic societies have powerful national-security bureaucracies, but a deep state is a bureaucracy that has more power than the political leaders it ostensibly serves. One former senior U.S. counterterrorism official described Pakistan’s problem this way: “Imagine if the CIA was supporting the drug cartels of Mexico over the wishes of the Congress and the White House,” he said. “That’s what we have in Pakistan.” We know what it means to be at war with a sovereign nation—but how should a country fight a deep state?

The notion of a deep state that seeks to subvert an established government is often the stuff of conspiracy theories, but in the case of Pakistan, it’s an accurate description of the way a faction of its government appears to function. The United States itself had a hand in the creation of Pakistan’s deep state. In the 1980s, Pakistan’s Inter-Services Intelligence Directorate (ISI) backed the Afghan mujahedin in their fight against the Soviet Union, with money and guidance from the CIA. But after the Soviets withdrew and the CIA shifted its focus elsewhere, the ISI kept supporting fundamentalist Islamic groups like Lashkar-e-Taiba (LeT) in order to advance Pakistani interests in India and Afghanistan. “For the ISI it was the start of institutionalizing the use of militant Islam as a political tool,” says Art Keller, a retired CIA case officer who served in the agency’s Waziristan base in 2006.

Thanks to Pakistan’s rivalry with India, the deep state grew deeper still. Jane Harman, who chaired the House Homeland Security Subcommittee on Intelligence until 2010 and is now the president of the Woodrow Wilson Center, says, “This all has to do with what we may call paranoia and what they would call justifiable fear about ... the role India could play in an Afghanistan that we might leave.”

For most of the war on terrorism, U.S. policy failed to account for the problem the deep state posed. In theory, the United States was supposed to ally with Pakistan’s military against terrorist groups. And, from 2001 to 2005, that alliance appeared to work. After the September 11 attacks, President Pervez Musharraf fired the leadership of Directorate S, the ISI bureau responsible for maintaining relations with the Taliban, LeT, and other jihadist groups. The ISI also played an important role in the capture of Al Qaeda leaders Abu Zubaydah, Ramzi bin Al Shibh, and Khalid Shaikh Mohammed. Over time, however, Pakistan’s vigilance waned, and the old ISI hands and military officers that had nurtured these terrorist groups reasserted themselves.

By 2005, the CIA began to accumulate evidence that the independent Taliban faction known as the Haqqani network was operating bases over the Pakistan border with ISI assistance. Keller says the CIA’s Kabul station urged its colleagues in Islamabad to minimize contact with the ISI. “Kabul felt the Pakistanis were totally dirty, and [the] Islamabad station was wasting their time until the Pakistanis stepped up to prove otherwise,” he says. Once, Keller recalls, he gave a Pakistani military officer information on a Haqqani network camp, only to learn that no senior terrorists were there when the military showed up—suggesting that they had been warned of the raid. “It yielded absolutely no one,” he told me.

Indeed, Pakistan’s tolerance for terrorists was becoming increasingly blatant. By 2006, the military had begun signing peace deals with Taliban-aligned tribes in the Federally Administered Tribal Areas (FATA)—effectively ceding the border region to the Pakistani Taliban and Al Qaeda. And the CIA noticed that western recruits were making their way to the FATA. “The heart of our analysis building from 2007 into 2008 was the increased safe-haven nature of the tribal region,” says Michael Hayden, who was CIA director at the time. “Many folks were going to the tribal region with western identities.” According to two former U.S. intelligence officers who worked on the Pakistan account, Directorate S, which had no formal relationship with the CIA, supported the safe havens.

The turning point in the U.S. relationship with the ISI came in 2008, after a suicide bomber attacked the Indian embassy in Kabul, killing more than 50 people, including an Indian defense attaché. The CIA concluded almost immediately that the ISI had planned the attack. “The attack on the Indian embassy is not just shadow boxing, spy versus spy,” says Ashley Tellis, who served as a South Asia policy adviser for the State Department. “This is a manifest attack which results in civilians dying, an attack on what is the sovereign territory of another country. It really begins to cross a threshold.”

After the Kabul attack, the CIA took a new and more cautious approach with the ISI, according to two U.S. intelligence officials as well as another American official. The agency restricted its relationship with the ISI to Directorate T, the counterterrorism division. At the same time, it began to develop its own human-intelligence-gathering capabilities inside Pakistan, using mainly contractors. Starting in the summer of 2008, the agency also stepped up its use of Predator and Reaper unmanned aerial vehicles in the FATA region.

By that time, the ISI appeared to be in open revolt against the U.S.-Pakistan alliance. On November 26, a team of LeT commandos terrorized the Indian port metropolis of Mumbai for three days. Last month, the Justice Department asserted that an ISI officer known as “Major Iqbal” gave money to an American who helped plan the Mumbai attacks. “After Mumbai, there was a massive what-the-fuck moment in the intelligence community,” a U.S. intelligence official says. “On the one hand you had Zardari [the current Pakistani president] and Kayani [the military’s chief of staff] wondering what happened. On the other hand, you had to have had a lot of people in the ISI know about something this big.” According to that official, the Office of the Director of National Intelligence released a report after the Mumbai attack containing dossiers for 30 or so senior Pakistani military and intelligence officers believed to be more loyal to terrorist groups than the official policies of the elected government.

When Barack Obama came into office, he built on the steps taken in the final years of the Bush administration to protect U.S. counterterrorism efforts from the pernicious effects of Pakistan’s deep state. Perhaps the most striking evidence of this is that the raid on the bin Laden compound was even kept secret from President Zardari until the mission was accomplished.

The raid was successful, but it has exposed the acute difficulty of pursuing an alliance with one part of the Pakistani government while working against another. The United States was able to prevent the deep state from thwarting its attack on bin Laden, but in doing so, it may have alienated the cooperative elements of the military. A week after the raid, a Pakistani newspaper printed the name of the CIA station chief—a leak that almost surely came from the ISI—and the army accused the United States of violating its national sovereignty. Meanwhile, the debate in Washington has mostly centered on whether or not to cut off the flow of aid money to Pakistan, which misses the point that the real problem runs much deeper.

Eli Lake is a contributing editor for The New Republic and national security correspondent for The Washington Times. This article originally ran in the June 9, 2011, issue of the magazine.

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