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For a covert spy agency, Pakistan's Directorate of Inter-Services Intelligence has been attracting a lot of attention. It's been rebuked by the U.S. government for failing to curb terrorism, accused in The New York Times of involvement in an international bombing, and targeted by the government it's supposed to serve — first for increased oversight, and now for a purge of its more extremist elements.

After years of denials, Pakistan admitted yesterday for the first time what others have been saying: There are "probably" still agents of Inter-Services Intelligence who are sympathetic to the Taliban and "act on their own in ways that are not in convergence" with Pakistan's interests or policies, Pakistani government minister Sherry Rehman said. "We need to identify these people and weed them out."

Anyone who has tracked the history of the ISI knows this is not a revelation, but a half truth. It's not individuals in the ISI that are rogue and working with the Taliban, but the ISI itself. The ISI, and the Pakistani army it serves, don't want to see the United States, and the government of Hamid Karzai, win in Afghanistan because they believe it would fatally undermine Pakistan's own national security, analysts say. The army does not trust U.S. intentions in the region, and it does not trust the Karzai government, which is close to India, Pakistan's giant and hostile neighbour.

"Nobody in Pakistan wants to see America win," said Hameed Gul, a retired general who is the most infamous former director-general of the ISI. "That would spell danger to Pakistan in the long run. They, America, want to make us subservient to India."

Earlier in the week, it had emerged that that the deputy director of the U.S. Central Intelligence Agency, Stephen Kappes, travelled to Pakistan in July, armed with documentary evidence of the ISI's role in supporting the Taliban in Afghanistan. In particular, he confronted the army chief, General Ashfaq Kayani, with proof of the agency's continued links with the Haqqani network, the group spawned by jihadi veteran Jalaluddin Haqqani, who, back in the 1980s, was a favourite of the ISI [and the CIA at the time].

Mr. Haqqani is wreaking havoc in Afghanistan again, and it will be nearly impossible for the Pakistani government to curtail support for him and others like him from within Pakistan.

That was made clear last weekend when Pakistan's recently elected government tried to place the ISI under firm civilian control, ordering that it report to the Interior Ministry. When Gen. Kayani was told of it, he placed a furious call in the middle of the night to Prime Minister Yousuf Razi Gilani to demand that the announcement be stopped. At 3 a.m., a new notification went out, reversing the decision.

The episode demonstrates that the ISI is beyond the reach of the government, certainly the present administration, which is viewed as weak and looks fatally wounded by the army's show of defiance over the agency's reporting structure.

"The ISI is under the policy directive of the man who calls the shots," said Shujaat Ali Khan, a retired general who used to head the internal wing of the ISI. "It may not be the Prime Minister, it may not be the President, but the army chief is always kept in the loop."

For three decades, the ISI has used Islamic extremist groups to do its dirty work at home and abroad, especially in India and Afghanistan. Its most famous creations were the mujahedeen that defeated a superpower, the Soviet Union, in Afghanistan in the 1980s, and the Taliban, which seized power in that country in the mid-1990s. But after Sept. 11, 2001, the ISI was supposed to have cut ties after Pakistan sided with the United States in the "war on terror."

Only it didn't. The links were loosened, but they remain, for the simple reason these militants are viewed as vital pawns in a bigger game: Keeping Afghanistan unsettled to limit the United States's — and by extension arch-rival India's —influence in the region.

The Taliban is merely the tool of a policy aimed at keeping Afghanistan from falling into the hands of Islamabad's adversaries, as Pakistan would be left sandwiched between two enemy states.

This is a military doctrine about national survival, not an ideology of religious fanaticism. Civilians are not welcome to meddle with it.

"If your perception, as the Pakistan army, is that RAW (the Indian intelligence agency) and the CIA are acting in unison, then you try to protect yourself," said Ayesha Siddiqa, author of Military Inc. "You do not give them [the Taliban] sufficient room to completely take over Afghanistan but you do enough to stop growing Indian influence."

Aside from the Haqqani network, other Taliban groups also seem to be working with a newfound energy and sophistication. Increasingly audacious Taliban attacks appear to point to the guiding hand of the ISI. Afghanistan has accused Pakistan of involvement in the mass prison break from Kandahar in June, and The New York Times reported yesterday that U.S. intelligence agencies had evidence of the ISI's hand in last month's bombing of the Indian embassy in Kabul, the deadliest attack in the Afghan capital since 2001.

While accusing fingers point to the ISI as a "state within a state," an organization that is dangerously out of control, any charges that are made against the agency should really be levelled at its boss, the Pakistani army itself.

Mr. Khan, the retired ISI general, rejected the idea that the ISI was still backing the Taliban, but he insisted that his former employer follows orders from the army.

"It's a very disciplined organization but with a very large freedom of action," he said. "When they get a policy directive, they have certain room for manoeuvre, keeping the interests of the state in view."

The Pakistani army needs to serve the United States — the only remaining superpower and the provider of billions of dollars of military aid — but it also has other, apparently contradictory, interests to promote, which the militants serve.

"The Pakistan army is like a woman with multiple lovers, she has to satisfy them all," Dr. Siddiqa said. "While courting the Taliban, it sleeps with America."

The picture is further complicated by the ideological evolution of the Pakistan-sponsored jihadists, which came under the more radical influence of al-Qaeda after Sept. 11. While it is believed that some militant groups, like the banned Jaish-e-Mohammad, remain more or less under the control of the ISI, others have come to regard the Pakistan state as their enemy, too. The ISI has created monsters that it cannot control.

"It's not a simple client-patron relationship," said Kamran Bokhari, director of Middle East analysis at Strategic Forecasting, a private U.S. intelligence firm. "The clients have their own agenda and room for manoeuvre. It's a very, very murky relationship and the attacks in Pakistan show that many operators have gone rogue."

The problem for the United States is that it needs Pakistan's help. Pakistani security forces, including the ISI, have captured more al-Qaeda operatives than anyone else and they are providing logistical and some military support in the fight against the Taliban in Afghanistan. The United States cannot just turn on Pakistan, so it is trying to build enough pressure on the country to force it to finally end its association with Islamic extremists. In short, it wants Pakistan to end the double game.

"The biggest issue is not what Pakistan is doing in Afghanistan, it is its unwillingness to target any militant organization on Pakistani soil," said Seth Jones, an analyst at Rand Corporation, a private U.S. research group.

Coalition commanders in Afghanistan have consistently complained that Taliban and al-Qaeda fighters find sanctuary on the Pakistani side of the border. Without cutting off refuge, supplies and training available to the militants in Pakistani territory, victory in Afghanistan looks nearly impossible.

"But the general assumption [in Washington] is that a mixed and unreliable ally is better than no ally at all," said Mr. Jones, who recently published a report on the Afghan insurgency commissioned by the Pentagon.

If Pakistani paranoia about India was the only thing that led its spies to work against the Karzai government, then it may be possible to provide reassurances and push back Indian activity in Afghanistan. However, beyond the fears about India are deep suspicions about U.S. intentions.

The fear, not only in the Pakistani intelligence community but across Pakistani society, is that, once the United States pacifies Afghanistan, Pakistan is next.