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Authors: Matthew M. Aid

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The glory days of U.S.-Pakistani intelligence cooperation came to an abrupt end in the fall of 2004, when ISI chief General Ehsan ul Haq was promoted to the position of chief of staff of the Pakistani armed forces. U.S.-Pakistani intelligence relations took a decided turn for the worse when Lt. General Ashfaq Parvez Kayani, now the Pakistani Army's chief of staff, took over as director-general of the ISI in October 2004. A chainsmoker and golfing fanatic, Kayani is a shrewd if not brilliant officer whose long experience in the upper echelons of the Pakistani military and high-level exposure to Pakistani politics (he had been the military assistant to Prime Minister Benazir Bhutto from 1988 to 1990) made him a gifted practitioner of the Machiavellian art of getting what he wanted by whatever means necessary.

Kayani quickly made his imprint on ISI. According to U.S. intelligence officials, beginning in 2004 the quality and reliability of the intelligence information that Washington received from the ISI, which was never very good to begin with, began to decline markedly. Shortly thereafter, sensitive intelligence sources confirmed that ISI was deliberately withholding from the United States increasing amounts of the intelligence that it had in its possession on al Qaeda activities in the FATA. A retired Pakistani intelligence official confirmed in an interview that Pakistan had, in his words, “dialed down” the amount of intelligence it gave the CIA because Washington was deliberately withholding from it equally important intelligence information.

U.S. intelligence officials confirm that there is truth in this allegation. CIA officials admit that the security regulations in effect at the time prevented them from giving the Pakistani government any intelligence information above the “secret” classification level, such as signals intelligence intercepts and sensitive human intelligence reports, all of which were classified at the “top secret” level.

But what galled the Pakistanis the most was that the CIA and U.S. military repeatedly refused to give the Pakistani military access to the live video feeds from CIA Predator and Reaper unmanned drones, which were flying reconnaissance and missile strike missions over northern Pakistan. In 2004, the Pakistani Air Force secretly made available for CIA Predator drones, real estate on two of its airfields, from which the agency flew armed combat missions attacking al Qaeda and Pakistani Taliban targets in the tribal areas of northern Pakistan. But the Pakistanis imposed very strict limitations on the drone flights. From 2004 to 2010, CIA drone missions over North and South Waziristan in northern Pakistan were permitted without any restrictions, but no flights over the neighboring province of Baluchistan and the Taliban command center of Quetta have ever been approved by the Pakistani government. The first missile strike by a Pakistani-based Predator drone occurred on June 18, 2004, near the town of Wana in South Waziristan, killing the leader of the local Pakistani Taliban, Nek Mohammed.
Over the next four years (2004–8), CIA Predator drones conducted
forty-six missile strikes on targets in the FATA, with the vast majority of the drone attacks taking place in the last year of the Bush presidency, 2008.

Pakistani military officials thought that since the drones were based at their airbases, and flying combat and reconnaissance missions in which Pakistani militants and civilians were being killed, then the very least that the CIA could do was let them know what intelligence was being derived from these missions that might assist their forces. They were doomed to be disappointed.
Senior Pakistani military officials asked for access
to Predator imagery at virtually every high-level meeting they had with their American counterparts, only to be politely but firmly rebuffed every time.

In recent interviews, Pakistani intelligence officials made clear that they have been aware for some time that the CIA station in Islamabad spent as much time spying on the activities of the Pakistani government and military as it did trying to find Osama bin Laden and his followers in northern Pakistan. According to Pakistani officials, they know that the CIA station has been operating a network of agents inside the Pakistani government and military since well before 9/11. A senior Pakistani official related how a few years ago a newly arrived U.S. Army intelligence officer, whose cover was as a military attaché at the U.S. embassy in Islamabad, approached a member of his paramilitary security unit and tried to recruit him by offering him a briefcase full of brand-new one-hundred-dollar bills. ISI officials were also certain that the CIA had installed highly sophisticated communications intercept gear inside the U.S. embassy in Islamabad and the American consulates in Peshawar, Lahore, and Karachi to intercept Pakistani government radio and telephone communications traffic.

So at some point after 2004, the ISI decided to treat the CIA station in Pakistan just like any other hostile intelligence presence operating in their country. The CIA's intelligence-gathering efforts inside Pakistan suddenly became much more challenging. CIA counterintelligence officers noticed that all U.S. diplomatic establishments in Pakistan were under twenty-four-hour-a-day video and electronic surveillance, and ISI surveillance teams were keeping close tabs on the movements of all CIA operatives in Pakistan. The home phones and personal cell phones of U.S. diplomats and CIA operatives in Pakistan were being tapped, their mail was opened, and their movements were closely watched. Even their personal cooks, maids, and porters were widely believed to be on the ISI payroll. Pakistani government and security officials who had cooperated with the United States were harassed, some even receiving anonymous death threats. The U.S. embassy in Islamabad complained about the hostile and obstructive behavior of Pakistani intelligence and security officials, but no remedial action was ever taken by the Pakistani government.

One CIA case officer just returned from a tour of duty in Pakistan recalled going with his family for a weekend drive in the hills outside Islamabad to escape the oppressive heat in the city. For the entirety of their day-long excursion they were followed by a black SUV with two ISI operatives inside watching their every move. When they stopped at a roadside stop to take in a scenic vista, the ISI surveillance vehicle parked a short distance behind them. The CIA man looked over, and both of the ISI agents were sitting inside their vehicle scanning the horizon with their binoculars trying to figure out what the Americans were looking at. The CIA officer and his wife laughed themselves silly all the way back to Islamabad.

In addition, ISI counterintelligence officers began systematically detaining the CIA's agents inside Pakistan, especially those individuals who were passing the CIA information from the al Qaeda and Taliban stronghold of the FATA in northern Pakistan. With the liberal application of less than gentle forms of persuasion, these individuals were coaxed, prodded, or cajoled into becoming double agents, feeding the CIA's Islamabad station with whatever material the ISI counterintelligence officers gave them.

It was not until late 2009 that the CIA became suspicious of the material they were getting from these agents and began an internal investigation. CIA counterintelligence officers discovered that at least fifteen of the agency's agents in the FATA were almost certainly under the “positive control” of the ISI, and that the reporting from another dozen or so operatives was sufficiently suspicious that the assets were “put on ice” for fear that they too were being controlled by ISI.

By the end of General Kayani's tenure at the helm of the ISI in the fall of 2007, the relationship between the Pakistani intelligence service and the CIA had deteriorated to the point that senior CIA officials were convinced that the ISI was penetrated by pro-Taliban sympathizers at all levels of command, leading Michael J. Sulick, then the head of the National Clandestine Service, to comment that “
they are going to cooperate [with the CIA] to the least extent that they can get away with
… That doesn't bode well in the search for Bin Laden.”

If the CIA's experiences with General Kayani were trying, the agency's problems with his successor, Lt. General Nadeem Taj, who was director-general of ISI from September 2007 to October 2008, were far worse.

By the time General Taj took over the helm of ISI, the joint CIA-ISI intelligence effort against al Qaeda in northern Pakistan was in trouble. Reporting from the CIA station and the U.S. embassy in Islamabad confirmed that
al Qaeda had succeeded in regenerating itself in the sanctuaries afforded it in northern Pakistan
. Despite the fact that there were fewer than a thousand al Qaeda militants in the FATA, the CIA and the Pakistani military and ISI could not get at them because the terrorists were protected by thousands of Pakistani Taliban fighters who had essentially cleared North and South Waziristan of all Pakistani military forces except for a few isolated garrisons, which the militants kept bottled up.

Beginning in the fall of 2007, several of the joint CIA-ISI intelligence operations in the FATA went horribly wrong. Sensitive intelligence information that the CIA was giving to the ISI on al Qaeda and Taliban activities in the FATA was found to be somehow leaking to the enemy, resulting in a number of CIA clandestine intelligence collection operations being compromised and agents either being killed or disappeared without a trace. Among the casualties were a number of important tribal chiefs and village elders in the FATA, who had been providing the CIA with intelligence on al Qaeda and Pakistani Taliban activities in their regions for some time.

Then in June 2008, the CIA station in Islamabad gave the ISI advance notice that it was going to use its unmanned drones to attack a compound in North Waziristan where a number of high-level Afghan Taliban commanders belonging to a faction known as the Haqqani Network had just been located. What the CIA did not know at the time was that the Haqqani Network and its chief, Jalaluddin Haqqani, had been on the ISI payroll for years. Not only was the ISI secretly bankrolling the Haqqanis, but according to a former CIA official, the Pakistani military was also covertly providing the organization with training, equipment, and logistical support. So not surprisingly, the ISI worked feverishly to delay the drone attack until they could get their clients out of harm's way. According to the CIA officer, the Pakistani Air Force officials at Shamsi Air Base in northwestern Pakistan, where the CIA Predator drones were based, were ordered by Islamabad to delay the takeoff of the drones because of “technical difficulties.” While the drones idled in their hangers at Shamsi, the Haqqani officials disappeared from the target locations, with intercepted cell phone calls revealing that they had been warned that they were about to be attacked just before they fled.

A few days later, on June 14, 2008, the CIA thought they had found the hideout of the leader of the Pakistani Taliban, Baitullah Mehsud, and told the Pakistanis they were going to hit the location with a drone strike. According to the CIA official, Mehsud mysteriously disappeared from the house shortly before three Hellfire missiles leveled it.

CIA officials were convinced that the targets of the strikes had been compromised from the inside, with the leaks appearing to come from the very top of the ISI. According to a former senior U.S. intelligence official now associated with a private security contractor, not only were General Taj and some of his deputies leaking sensitive information to the Haqqani Network, as well as elements of the Pakistani Taliban, about ongoing CIA operations in northern Pakistan; sensitive intelligence showed that these same Pakistani intelligence officials also were fully cognizant of the fact that ISI officers in the FATA were providing weapons and logistical support to the Taliban.

The leaks emanating from the top of the ISI forced the U.S. intelligence community to take what some in Washington at the time considered to be extreme measures. A few days after the July 7, 2008, suicide bombing of the Indian embassy in Kabul, which killed forty-one people, CIA director General Michael Hayden gave President Bush a target list of the several dozen al Qaeda and Taliban operatives that the agency had located inside northern Pakistan and wanted to kill. Near the top of the list was the entire senior leadership of the Haqqani Network, which was widely suspected by the CIA of being behind the Indian embassy bombing.

A few mid-level American intelligence officials opposed the new policy, arguing that instead of killing al Qaeda operatives, some effort should be made to try to capture these men if and when the opportunity presented itself. According to two former CIA counterterrorism officials, because no senior or even mid-level al Qaeda official had been captured for several years prior to the initiation of the policy, the CIA's knowledge of al Qaeda's internal organizational structure and management dynamics, as well as the group's plans and intentions, remained very spotty. But their appeals were rejected on purely utilitarian grounds. According to a senior U.S. intelligence official interviewed in 2009, “Capturing al Qaeda officials is a bother. It is so much easier just to kill 'em when you find them.”

Without consulting the Pakistani government or military, President Bush approved Hayden's request to use both military commando raids and CIA Predator drone strikes to kill the individuals on the list, which CIA officials refer to privately as either the “Kill List” or the “Murder List.” Within hours of President Bush signing the top secret authorization, the CIA operations center at Langley sent a “flash” precedence message giving the go order to the Predator drones based in Pakistan. In a 2010 interview, Hayden said that
“by the time I left office (in January 2009), more than a dozen of those people [on the list] were dead.”

But the new round of CIA attacks also produced some particularly horrific collateral damage. For example,
shortly before dawn on the morning of September 3, 2008
, a twenty-five-man U.S. Special Forces team was landed inside Pakistan by helicopters near the remote border village of Angoor Ada to capture or kill the occupants of what was believed to be an al Qaeda safe house. No one seems to know for sure who the al Qaeda target of the raid was, but whoever it was he seems to have escaped. The local villagers were not so lucky. According to Pakistani officials, at least nineteen civilians were killed in the raid, including women and children.

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