Islamabad's relationship with the Taliban-affiliated Haqqani network has precipitated a crisis in its relationship with Washington.

In 1992, nine full years before 9/11, the Pakistani Islamist politician Fazlur Rahman laid out a road map for the global jihadist magazine. “The Afghan jihad,” he told the Pashto language Manba al-Jihad magazine, “which was spearheaded by Maulana Haqqani and other truthful leaders, defeated the Soviet empire. But now there is another enemy to this jihad. That is America, and its conspiratorial policies that are intended to bring Afghanistan, the centre of jihad, under American attack.”

Fazlur Rahman concluded: “we are absolutely certain that people like Mawlawi Haqqani will give the Americans the same answer they gave to the Russians. And we are sure that people like Haqqani will fuel the flames of jihad worldwide.”

The assassination of Burhanuddin Rabbani, Afghanistan's former President and principal negotiator for talks with jihadists, has underlined the abiding threat from the immoderate Taliban: Afghan groups closely entwined with the global jihadist movement, hostile to dialogue — and, yet, backed by Pakistan, which sees them as allies in its own battle for survival.

Last week, in the wake of a terrorist assault targeting the United States Embassy in Kabul, the U.S. held out its most blunt warning yet to Pakistan, the principal patron of Islamist warlord Sirajuddin Haqqani, son and heir apparent to the man Fazlur Rahman hailed. “I think the message they [the Pakistanis] need to know,” said Defence Secretary Leon Panetta, is that “we're going to do everything we can to defend our forces.” In Islamabad and Washington alike, that phrase has been read as a threat to use force inside Pakistan.

For years now, U.S. officials have privately used similar language. The Haqqani network is not just responsible for most major strikes in Kabul — among them, the murderous 2008 attack on the Indian Embassy — but also part of the reason why western efforts to engage purported moderates in the Taliban have gone nowhere. Now, as the U.S. prepares to dramatically scale down its presence in Afghanistan, it needs Pakistan to act against the Haqqanis more than ever.

That, in turn, makes a showdown between the U.S. and the country its former military ruler Muhammad Ayub Khan once described as its “most allied ally” seems evermore likely.

‘The fountainhead of jihad': Born in the early 1950s, Jalaluddin Haqqani hailed from the Zadran tribe of the Pashtun ethnic group. He studied at a seminary in Datta Adam Khel, and would likely have gone on to become a rural cleric — had it not been for a series of dramatic events that transformed Afghanistan, eventually bringing to power a new class of armed clerics who would displace both the traditional tribal élite and the modernising left-wing secularists who had swept them aside.

In 1973, Afghan communists overthrew the decaying monarchy. Even though the new President, Daud Muhammad Khan, was the deposed king's brother-in-law, he declared the country a republic. President Khan presided over a dramatic process of social reform — marked, among other things, by an emphasis on women's rights. Pakistan's Inter-Services Intelligence (ISI) Directorate, fearful that Mr. Khan's nationalist rhetoric would seduce ethnic Pashtuns living on its side of the border, responded by backing an insurgency spearheaded by the Afghan Islamists.

Five years before the crisis that would suck the Soviet Union into Afghanistan, Jalaluddin Haqqani declared war against the Afghan state. Helped by the ISI, he developed sources of funding in the Middle East, using the flow of cash to build an impressive military apparatus.

The ISI, though, wasn't Jalaluddin Haqqani's only source of support. In the wake of the Soviet intervention in Afghanistan, journalist Steve Coll has revealed, he was cultivated as a Central Intelligence Agency (CIA) asset. Charlie Wilson, a right-wing politician who helped funnel tens of millions of dollars to the Afghan jihadists, described Jalaluddin Haqqani as “goodness personified.”

Key figures in the global jihadist movement — among them Osama bin Laden — learned their military skills in camps set up by Jalaluddin Haqqani, and maintained a close relationship with him in the years that followed.

Mustafa al-Hamid, an al-Qaeda linked ideologue and writer who served with Jalaluddin Haqqani's forces, wrote a hagiographic account which was published in the jihadist magazine al-Somud last year. The “majesty in his personality was a model for the great religious scholars of Afghanistan and students of the knowledge of the pure mujahideen, who now stand as an impregnable bulwark against the largest crusader attack upon the Islamic nation.”

From the outset, scholars Don Rassler and Vahid Brown have noted in a seminal paper, that Jalaluddin Haqqani helped shape the global jihadist movement's ideas.

In 1980, for example, Haqqani asserted that Middle Eastern charity to the Afghan campaign did “not absolve the individual Muslim of the duty to offer himself for the jihad.” Abdullah Azzam — bin Laden's mentor, Lashkar-e-Taiba co-founder and ideological patriarch of the global jihadist movement — arrived at the same conclusion four years later, when he declared the Afghan jihad fard ‘ayn, an individual obligation. When bin Laden shifted base to a pink stucco three-storey home in Khartoum in 1991, having fallen out with Saudi Arabia's royal family, Jalaluddin Haqqani used the opportunity to operate on a wider stage. He backed Hasan al-Turabi's Islamist regime in Sudan, and sent volunteers to fight in Bosnia. In 1991, at a meeting in Karachi, he also bragged about his war against India, saying his networks had “trained thousands of Kashmiri mujahideen and have made them ready for the jihad.”

Nizamuddin Haqqani, Jalaluddin Haqqani's deputy, proclaimed in 1991 that the U.S. and Russia were “both infidel forces.”

The resurgent warrior: Bin Laden's close relationship with the Haqqanis helped him act on those ideas during his last, tortured months in Afghanistan — scarred by an increasingly bitter relationship with Taliban chief Mullah Muhammad Omar which saw al-Qaeda's leader confined to the city of Kandahar.

“From that point on,” Dr. Rassler and Dr. Brown record, “al-Qaeda came to increasingly rely on the Haqqani network's autonomy from the Taliban in Loya Paktia as a launching pad for its declarations of war on the West.”

Bin Laden's declaration of jihad against the West — his most sweeping manifesto and ideological keystone of the 9/11 attacks, was critically issued from a Haqqani camp in the Zhawara valley.

Since 9/11, the Haqqani network has survived by using the same geographical advantages that stood it so well during the anti-Soviet jihad: its control of key routes from Pakistan into Afghanistan, and its ability to retreat south across the border. Much of the organisation is now run out of Miranshah, deep inside Pakistan's North Waziristan region. Ever since Sirajuddin Haqqani started taking care of the organisation, it has expanded out of its Loya Paktia strongholds into Nangarhar and Kunar, and southward to Ghazni — even while insisting that it is a part of the Islamic Emirate of Afghanistan, as the Taliban calls itself.

Mullah Omar has often been reported to resentful of the Haqqani network's autonomy — but there is no sign of any friction on the ground. “This,” Dr. Antonio Giustozzi, an academic, pointed out, “is clearly not the reaction one would expect if the Haqqani network was seen by the Taliban leadership in Quetta as a separate, competing organisation.”

Put another way, the power of the Haqqanis suits the broader Taliban. More important, it suits Pakistan, too.

The reasons are none-too-opaque. In return for ISI patronage, it has proved a valuable source of support in Pakistan's north-west — the heartland for jihadists hostile to the state. Sirajuddin Haqqani is believed, for example, to have brokered the February peace deal in Kurram, which brought about a brief cessation of hostilities between Shi'a and Sunni militia. He, along with other “good Taliban” like Gul Bahadur and Maulvi Nazir Ahmad, is also seen as a source of pressure on Tehreek-e-Taliban leaders like Hakimullah Mehsud.

In the long-run, Pakistan's strategic establishment believes that bringing allies like Sirajuddin Haqqani to power in Kabul will help it contain the jihadist threat to its own survival. Increasingly, Pakistan's strategic community is arguing that the Haqqanis' ambitions are local — not a threat to the world.

How well-advised this calculation will prove remains unclear. Ever since 9/11, Dr. Rassler and Dr. Brown have noted, it has changed course, portraying itself “as a local actor preoccupied with local concerns.” This message, though, changed depending on the audience. In the Pashto and Urdu language versions of the journal Nusrat al-Jihad, for example, the role of Arabs in the famous 1991 siege of Khost is ignored. However, the Arabic language version celebrates their contributions.

Key figures in Pakistan's “good Taliban” have been less coy. In an interview this May, for example, the Pakistani army's ally, Nasir Ahmad, announced that he was “a part of al-Qaeda.” He argued that events in the Middle East would “benefit the mujahideen” and promised to despatch jihadists to “join forces with the Arabs.” It takes little to see that Pakistan's jihadist allies could precipitate precisely the same kind of problems that created the crisis it is now fighting.

This we know for certain: the U.S. has spent years pressing Pakistan to act, without effect. In diplomatic cables obtained by the WikiLeaks, there is a graphic account of a July 29, 2008, meeting between top U.S. officials and Pakistan's Prime Minister, Yousaf Raza Gilani. Anne Patterson, Washington's Ambassador to Islamabad, hit out at Pakistan's claims that it had no knowledge of Sirajuddin Haqqani's whereabouts. She asserted that the ISI was in “constant touch” with him, and that the seminary from where he conducted business was clearly visible from a Pakistani military base.

Now though, as the U.S. prepares to withdraw from Afghanistan, it no longer has the luxury of time — and that means Pakistan could soon be faced with hard decisions, each with murderous consequences.