C.I.A. and Pakistan Work Together, Warily

ISLAMABAD, Pakistan — Inside a secret detention center in an industrial pocket of the Pakistani capital called I/9, teams of Pakistani and American spies have kept a watchful eye on a senior Taliban leader captured last month. With the other eye, they watch each other.

The C.I.A. and its Pakistani counterpart, the Directorate of Inter-Services Intelligence, have a long and often tormented relationship. And even now, they are moving warily toward conflicting goals, with each maneuvering to protect its influence after the shooting stops in Afghanistan.

Yet interviews in recent days show how they are working together on tactical operations, and how far the C.I.A. has extended its extraordinary secret war beyond the mountainous tribal belt and deep into Pakistan’s sprawling cities.

Beyond the capture of Mullah Abdul Ghani Baradar, C.I.A. operatives working with the ISI have carried out dozens of raids throughout Pakistan over the past year, working from bases in the cities of Quetta, Peshawar and elsewhere, according to Pakistani security officials.

The raids often come after electronic intercepts by American spy satellites, or tips from Pakistani informants — and the spies from the two countries then sometimes drive in the same car to pick up their quarry. Sometimes the teams go on lengthy reconnaissance missions, with the ISI operatives packing sunscreen and neon glow sticks that allow them to identify their positions at night.

Successful missions sometimes end with American and Pakistani spies toasting one another with Johnnie Walker Blue Label whisky, a gift from the C.I.A.

The C.I.A.’s drone campaign in Pakistan is well known, which is striking given that this is a covert war. But these on-the-ground activities have been shrouded in secrecy because the Pakistani government has feared the public backlash against the close relationship with the Americans.

In strengthening ties to the ISI, the C.I.A. is aligning itself with a shadowy institution that meddles in domestic politics and has a history of ties to violent militant groups in the region. A C.I.A. spokesman declined to comment for this article.

Officials in Washington and Islamabad agree that the relationship between the two spy services has steadily improved since the low point of the summer of 2008, when the C.I.A.’s deputy director traveled to Pakistan to confront ISI officials with communications intercepts indicating that the ISI was complicit in the bombing of the Indian Embassy in Kabul, Afghanistan.

The spy agencies have built trust in part through age-old tactics of espionage: killing or capturing each other’s enemies. A turning point came last August, when a C.I.A. missile killed the militant leader Baitullah Mehsud as he lay on the roof of his compound in South Waziristan, his wife beside him massaging his back.

Mr. Mehsud for more than a year had been responsible for a wave of terror attacks in Pakistani cities, and many inside the ISI were puzzled as to why the United States had not sought to kill him. Some even suspected he was an American, or Indian, agent.

The drone attack on Mr. Mehsud is part of a joint war against militants in Pakistan’s tribal areas, where C.I.A. drones pound militants from the air as Pakistani troops fight them on the ground.

And yet for two spy agencies with a long history of mistrust, the accommodation extends only so far. For instance, when it comes to the endgame in Afghanistan, where Pakistan hopes to play a significant role as a power broker, interviews with Pakistani and American intelligence officials in Islamabad and Washington reveal that the interests of the two sides remain far apart.

Even as the ISI breaks up a number of Taliban cells, officials in Islamabad, Washington and Kabul hint that the ISI’s goal seems to be to weaken the Taliban just enough to bring them to the negotiating table, but leaving them strong enough to represent Pakistani interests in a future Afghan government.

This contrasts sharply with the American goal of battering the Taliban and strengthening Kabul’s central government and security forces, even if American officials also recognize that political reconciliation with elements of the Taliban is likely to be part of any ultimate settlement.

Tensions in the relationship surfaced in the days immediately after Mullah Baradar’s arrest, when the ISI refused to allow C.I.A. officers to interrogate the Taliban leader. Americans have since been given access to the detention center. On Wednesday, Pakistani and Afghan officials meeting in Islamabad said that a deal was being worked out to transfer Mullah Baradar to Afghan custody, which could allow the Americans unrestrained access to him.

Besides Mullah Baradar, several Taliban shadow governors and other senior leaders have been arrested inside Pakistan in recent weeks.

A top American military officer in Afghanistan on Wednesday suggested that with the arrests, the ISI could be trying to accelerate the timetable for a negotiated settlement between the Taliban and the Afghan government.

“I don’t know if they’re pushing anyone to the table, but they are certainly preparing the meal,” the officer said.

In the three decades since the C.I.A. and the ISI teamed up to funnel weapons to Afghan militias fighting the Soviets, the two spy services have soldiered though a co-dependent, yet suspicious relationship. C.I.A. officers in Islamabad rely on the Pakistani spy service for its network of informants. But they are wary of the ISI’s longstanding ties to militants like the Taliban, which Pakistani spies have seen as a necessary ally to blunt archrival India’s influence in Afghanistan.

The ISI gets millions of dollars in United States aid from its American counterpart (which allowed the Pakistan spy service to develop a counterterrorism division), yet is suspicious that the Americans and the Indians might be playing their own “double game” against Pakistan.

In Islamabad, officials are nervous about the intensification of the C.I.A.’s drone campaign in North Waziristan against the network run by Sirajuddin Haqqani, whom the ISI for years has used as a force to carry out missions in Afghanistan that serve Pakistani interests.

C.I.A. officials believe that Mr. Haqqani’s group played a role in the killing of seven Americans in Khost, Afghanistan, in late December, and since then have carried out more than a dozen drone strikes in the Haqqani network’s enclave in North Waziristan.

The ISI, an institution feared by most Pakistanis, is used to getting its way. It meddles in domestic politics and in recent months has been suspected by Western embassies in Islamabad of planting anti-American stories in Pakistani newspapers.

It has also been criticized in reports by international human rights organizations of using brutal interrogation tactics against its prisoners, though the same could certainly be said of the C.I.A. in the period of 2002 to 2004. The annual human rights report of the State Department in 2007 said “there were persistent reports that security forces, including intelligence services, tortured and abused persons.”

The head of the Pakistani military, Gen. Ashfaq Parvez Kayani, said in a recent briefing that it was doubtful that a centralized government would work in post-conflict Afghanistan, making it more important for Pakistan to continue to influence the Taliban in the years to come.

As a result there remains a belief among American intelligence officials that Pakistan will never completely abandon the Taliban, and officials both in Washington and Kabul admit that they are almost completely in the dark about Pakistan’s long-term strategy regarding the Taliban.

“We have a better level of cooperation,” said one top American official who met recently in Islamabad with General Kayani. “How far that goes, I can’t tell yet. We’ll know soon whether this is cooperation, or a stonewall and kind of rope a dope.”