Killing ourselves in Afghanistan

While Muhammed was contemplating defection, U.S. intelligence officials were growing frustrated with the duplicity of a supposed ally in the war on terror, and with the limitations placed on them by Islamabad and Washington. But much of the problem was due, initially, to the way the CIA conducts its business, and to the rules of engagement in the Afghan-Pakistan border region.

The CIA rotates most of its officers in the area every three to six months, giving them insufficient time to learn the contours of Pakistan's problems. Virtually no operational officers speak Pashtun, nor can they travel without an official Pakistani escort.

Also, until recently, the CIA division of labor has made officers in Afghanistan responsible for attacking and thwarting Taliban inside Pakistan. Officers based in Pakistan are primarily tasked with tracking al-Qaida and Arab terrorists inside Pakistan.

Since the war began the general rules of engagement for U.S. forces -- be they CIA or other -- was that military attacks inside Pakistan could extend only six miles from the border, and only in pursuit. Attacking or even surveying training camps and any insurgent movements aided by Pakistan army units more than 20 miles inside the border was an impossibility.

Simply understanding the political dynamics of the Tribal Areas and the rest of Pakistan's frontier region to the north was therefore slow and laborious for American officials. Interference from the Pakistanis has made it still more difficult. CIA officers in Pakistan, who outnumber those stationed in Afghanistan, are not allowed to travel in Pakistan's frontier areas without ISI accompaniment. A retired CIA officer, who still works on contract for the agency, told me that in early 2006, he was based in Dir, a restive area north of North Waziristan in Pakistan's North-West Frontier Province, and not far from several U.S. bases in Afghanistan. The contractor was part of a joint CIA-ISI team hunting for bin Laden and al-Zawahiri. Before his rotation ended he asked the ISI brigadier if they could fly still farther north to the town of Chitral to watch some of the region's famed polo tournaments. "This guy told me straight up, 'I ain't letting you go north.'" The American persisted and was again rebuffed. "I realized that the only two reasons he wouldn't let me travel north was because he either was afraid of what I would see, or he was afraid of what he would see."

The Americans were quickly aware that the Pakistanis had no enthusiasm for fighting the Islamist insurgency. Gary Schroen, a former senior CIA official who led the first U.S. team into Afghanistan days after 9/11 and a former station chief in Islamabad, told me recently that where the Pakistan army does engage in battle against militants, they do so without vigor. "The Pakistanis don't want to fight a counter-insurgency inside their own country," he said. "They don't want to fight against Muslims, they want to fight against India."

According to a former senior government official responsible for U.S.-Pakistani policy, many American policymakers took for granted Musharraf would work harder going after al-Qaida than going after the Taliban. "I always assumed that, strategically, Pakistan would want to hedge its bets for the day the U.S. decided to pull out of the region." Pakistan had helped create the Taliban years earlier as an element of its regional security plan, meaning, in part, as an additional Muslim counterweight against perennial foe India. The U.S. expected a certain lack of enthusiasm from the Pakistanis for pursuing the Taliban, or at least a greater enthusiasm for dealing with al-Qaida. But Pakistan actually remained committed to keeping the Taliban active inside Afghanistan. What's more, said the former senior official, the White House had no mechanism for determining whether the ISI or other factions within the Musharraf regime were aiding the Taliban. Washington was conducting a "see no evil" foreign policy.

Ultimately, the Americans came to realize that the ISI was not just avoiding conflict with the insurgents, or shielding them, but actively abetting them. The senior American policy advisor told me that U.S. intelligence concluded that the ISI support -- often in the form of medical aid, signals intelligence and military strategy -- is not the work of rogue officers within Pakistan intelligence. "Injured Taliban fighters have been sent to military hospitals for good medical care," he said. "That doesn't happen inside Pakistan unless the military knows." Some ISI agents were attempting to help the Americans catch insurgents, but the most powerful faction within the agency was doing precisely the opposite.

The ISI has two main divisions. The CIA works primarily with Directorate C, the ISI's version of a counter-terrorism branch. According to a former senior CIA official who still reads intelligence reports from the region, Directorate C has been penetrated by American intelligence and its leader vetted by the CIA.

A second and much larger division of the ISI, however, is Directorate S, which is responsible for external operations, such as Afghanistan, Kashmir and India. It takes precedence over Directorate C, and often works at cross-purposes. The CIA has no working relationship with Directorate S, and no means to assess the loyalty of its personnel. A retired CIA officer who once served in the Tribal Areas recounted an exchange with his ISI partner from Directorate C. "He told me that he had just gone to a tribal shura in Peshawar and sat across from a man he'd arrested and imprisoned a few weeks earlier. He was convinced the man was a Pashtun terrorist. He said that one of his peers from Directorate S had released him within a few days -- with no notice or paperwork.

"This guy was trying to commiserate with me about how difficult it was to get anything done in the Tribal Areas," said the CIA officer. "He was truly frustrated. A few weeks after nabbing a bad guy, he had to sip tea and negotiate with him."

But the Americans discovered that the ISI was able to create some plausible deniability for its role in promoting the Taliban insurgency by relying on a Pakistani version of Blackwater. After 9/11, some ISI officers who were deemed too sympathetic to Islamic extremism were purged from the agency as a condition of American aid. These officers were never truly purged, however, and with other former and retired ISI agents form an extra-governmental conduit for ISI aid to the anti-American insurgents in the border area. Newsday reported last year that "the ISI offers the insurgents tactical advice and information about the deployment of U.S. forces."

As an example, the CIA learned that since 2005, a retired ISI officer who lives within 10 miles of the Afghan border, not far from a U.S. fire base, and who helped arm Afghan jihadists against the Soviets in the 1980s, was again working for the ISI -- this time on contract. According to U.S. and Afghan sources, this man, whom the CIA refers to as "General Yusef," recruits and organizes Afghan men to fight in Afghanistan's Nuristan and Kunar provinces. He is officially retired but reports to an ISI office in Chitral and receives a monthly stipend. For the ISI, General Yusef and his privatized peers are the perfect tools to help destabilize Afghanistan, since they don't officially work for the ISI.

General Yusef was responsible for procuring some of the fighters based at a training camp in Chitral that was the source of a spate of attacks on U.S. bases. The ISI, meanwhile, was responsible for the camp's very existence. In late 2006, Taliban and insurgent attacks on U.S. forces were escalating along the northern Afghan-Pakistani border. CIA officers stationed in northeast Afghanistan began to receive raw intelligence that a small but effective training camp had opened across the border in Chitral. The camp was run by the terrorist group Laishka-e-Taiba (LeT), which had been formed in the late 1990s by the ISI as a proxy force of jihadists to fight hundreds of miles to the east against the Indian government in Kashmir, the province over which India and Pakistan have been fighting for 60 years.

Next page: "CIA had worked on this thing for some time, and the son of a bitch tipped Haqqani off"