Is Pakistan Losing Patience in the War on Terror?

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Anjum Naveed / AP

Kareem Khan, center left, a Pakistani tribesman from North Wazirstan at a press conference in Islamabad on Nov. 29, 2010

On Saturday, in answer to a New York Times article, Pakistan's secretive spy agency denied that it had exposed the identity of a senior CIA official in Pakistan, causing him to abruptly leave Pakistan. In a briefing held on background, an official of the Directorate for Inter-Services Intelligence (ISI) couldn't have made it more categorical: "We absolutely deny this accusation, which is totally unsubstantiated and based on conjecture."

Short of a smoking gun, we'll have to take the Pakistanis' word for it. CIA cover is never perfect, and this wouldn't be the first time that a CIA officer has been forced to leave his post in the middle of the night.

But what can't be dismissed is the suit filed by a Pakistani tribesman in which he accuses the CIA of murdering his brother and his son in a drone attack. According to press reports, none of which have been confirmed by the CIA, it was the appearance of the station chief's name in a filing in this suit, along with unspecified threats, that caused him to be pulled. Regardless, the suit itself could be an ominous sign that the Pakistanis may be coming to the end of their rope in the "war on terror."

Here's why: I have long known that the ISI oversees the judiciary, from the appointment of judges to interfering in cases that harm national security. There are no exceptions. If there were a Julian Assange, the WikiLeaks founder, he'd be behind bars — for life. In other words, it's all but certain that the ISI greenlit the case brought by the tribesman for the death of his brother and son.

The ISI's power in the judiciary hit home for me two years ago. My wife and I were winding our way through the Pakistani court system as part of an adoption. I wondered right from the beginning how often ex-CIA agents had appeared before Pakistan's notoriously conservative judiciary - and what the government would think about us, or if it might even block the adoption. Every lawyer I talked to assured me that the government - the ISI - wouldn't care about a civil case. When I asked whether the ISI intervened in cases touching national security, they only smiled.

In trying to figure out what's happening in Pakistan these days let's not fool ourselves. The ISI is not a rogue agency that does exactly what it wants. It falls squarely under Pakistan's military. The commander and chief controls the budget as well as personnel appointments. At any time, he can remove the ISI's director. And since Pakistan's military is the ultimate executive authority in the country, it would be safe to conclude Pakistan itself permitted the suit against the CIA.

Conceding that I've climbed out on a long speculative limb — but who doesn't when it comes to Pakistan? — we should be wondering just how much purchase we've lost in Pakistan. They want our money, but not our drones. They don't want the United States to fall into the arms of India, but they also do not intend to kowtow to us. They want to be a part of any settlement in Afghanistan, but they won't or can't bring the Taliban under control. But now, with leading elements of the country possibly going after the CIA, whether it's by leaking a name or by fighting it in the courts, we should start wondering whether Pakistan is done with the bargaining on the war on terror.

Baer, a former Middle East CIA field officer, is's intelligence columnist and the author of See No Evil and, most recently, The Devil We Know: Dealing with the New Iranian Superpower