The Secret History of US-Pakistan Relations

The modern relationship between Pakistan and the US can be traced back to a significant starting place: Afghanistan. Modern Afghanistan is divided by Hindu Kush mountain range stretching across the middle of the country. To the south live mainly Pashtun tribes, intermingled with Persian-speaking ethnic groups, and towards the north of the country live the Tajiks, Uzbeks, Hazaraas, Turkmen and others, with agriculture the mainstay for most. Religious faith and ethnic identity in Afghanistan reflects the country’s political geography: a patchwork of diversity, decentralized rule, and local personalities that reflect the legacy of centuries of invasion and occupation.Throughout much of the twentieth century, the country was governed in relative harmony by a succession of Kings.

This changed in Kabul during the 1960s, when radical doctrines began to permeate the university population, dividing students between KGB-supported Marxist texts and the political manifestos of the Muslim Brotherhood (imported from Jedda, Saudi Arabia). These ideas  resonated politically: in 1965 the Afghan Communist Party was secretly formed, led by Babrak Karmal and Nur Mohammed Taraki. Throughout this period, Sardar Mohammed Daoud Khan was Prime Minster (1953 to 1963)  and later the first President of Afghanistan, after overthrowing the monarchy of his first cousin Mohammed Zahir Shah on July 17, 1973. In April 1978 he was killed in a communist coup, with Nur Mohammed Taraki taking control. He stated that their policies were rooted in Islamic principles and Afghan nationalism, but the hard-line Marxist rule alienated and angered the traditional Pashtun population. Millions fled to Pakistan, were hundreds of madrassas were being constructed by Pakistani intelligence in and around Peshawar, Quetta, and Karachi. The largest of these religious schools was Haqqannia, which attracted tens of thousands to its theological mix of Indian Deobandism and austere Saudi Wahhabism. This religious and military training on the Afghan frontier would provide the imagination and skills for the mujahideen that was about to grip the country. A power struggle between Taraki and his Deputy Prime Minister Hafizullah Amin, culminated in Taraki’s death on September 14, 1979.

In response to this growing political turmoil, the USSR invaded Afghanistan on December 24 to buttress the faltering communist regime: executing Amin and installing Moscow-friendly Babrak Karmal as leader. Millions of Afghans fled to neighbouring Pakistan and Iran. Not only did the arrival of thousands of Soviet troops concern Pakistan, who long saw Afghanistan as vital to its ‘strategic depth’ in the region and feared Pashtun independence; the Cold War ensured that Washington D.C. was soon briefed. The CIA first sent proposals to support the anti-communist Afghan mujahideen to Jimmy Carter’s White House in March 1979. On July 3, 1979, Carter signed a Presidential ‘finding’ that authorized the CIA to spend just over $500,000 to support the rebellion. But the CIA was not permitted to send funds to the mujahideen directly (nor would it want to reveal its fingerprints to the Soviets), so it went through the Inter-Services Intelligence Directorate (ISI), headed by Director General Akhtar Abdur Rahman, the main liaise with the CIA’s Islamabad station Chief, Gary Hart.

The ISI would remain the CIA’s main intermediary for a decade, growing in power as it was fed by millions of US dollars. President Zia saw the madrassas as a vital and secretive geopolitical weapon against Afghanistan communism and Indian occupation of Kashmir. Yet the consequence of this proxy war for the CIA was that its foreign policy became the ISI’s foreign policy; its clients the CIA’s clients. The ISI’s choice warlords were Muslim Brotherhood figures like the extremist Hekmatyar and his Hizb-e-Islami, together with Sayyaf, Rabbani, and Haqqanni (all of which isolated Mohammed Shah Massoud in the Panjshir valley to the north of Afghanistan). They were all trained by Lt.-Gen. Naseerullah Babar, the head of the paramilitary Frontier Corp. Babar would later become an important figure in launching the Taliban in the mid-1990s. Millions of dollars were transformed into hundreds of training camps, with the hope that those fighters would bring down the Soviet war machine. And they did. By 1984, mujahideen warriors, funded by William Casey’s CIA and Akhtar’s ISI, exalted by Ronald Reagan and President Zia, had killed or wounded 17,000 Soviet soldiers, controlled 62 percent of the country, and destroyed thousands of trucks and tanks. The secret war had only cost the US $200 million so far, but the Soviet’s had sunk $12 billion into a losing battle. Emboldened by these numbers, the CIA experienced a funding surge in October 1984: gaining $250 million in a single year (Coll, 2004).

The CIA’s covert operation in Afghanistan escalated further in 1985 after National Security Decision Directive 166, which would allow teams to enter Afghanistan directly, and lead to enormous budgets for secret operations. A ‘Counterterrorist Center’, located within the CIA’s Directorate of Operations was also born on February 1986 to combat terrorism, and accompanied by another piece of legislation: National Security Decision Directive 207, which gave the CIA even more power to undertake secret operations to pre-empt and detect terrorist activity. In 1986, the US Congress secretly allocated $470 million in US funding for Afghan covert action, rising to $630 million in 1987. All of which meant that by 1986, Brigadier Yousaf of the ISI had constructed a massive secret infrastructure for guerrilla training along the border, with between 16,000 and 18,000 recruits passing through the camps each year, with thousands of them heading to the battlefield. By the summer of 1988 there were about eight thousand official religious schools and an estimated twenty-five thousand unregistered ones. Influential figures like Haqqani and Sayyaf, who straddled the border region where CIA money was most flush, were by 1989 organizing Arab volunteers to fight the mujahideen. Between 1982 and 1990, the secret arms of the US, Saudi Arabia, and Pakistan, funded the training of some 35,000 Islamic militants from 43 Muslim countries in Pakistani madrassas to fight the Soviets. All of it was too much for the Soviets, who withdrew in 1989. But their proxy government headed by Najibullah clung on to power for years after, despite ISI attempts to install their client Hekmatyar.

CIA money and influence faded in the region throughout the 1990s as Afghanistan was more or less abandoned as the Cold War thawed. On January 1st, 1992 both US and Soviet ministers pledged they would halt support to their favored proxies, and there would be no CIA Chief assigned to Afghanistan until the autumn of 2001. It was throughout the 1990s under the Clinton Administration that the CIA’s intelligence on Afghanistan was at its lowest. Afghanistan was a massive blind spot, despite the incredible volume of covert operations only years earlier. But the hundreds of thousands of fighters that the CIA and ISI had funded remained, and the country would soon descend into civil war, as Massoud and Hekmatyar vied for control of Kabul. The former claimed a bloody victory and became defense minister under the short-lived government of Professor Rabbani in 1992. All the while, Osama bin Laden was establishing Afghanistan as the base for his al-Qaeda, among the architecture, materiels, and spaces from the smoking ruins of a mujahideen backed by the US, Saudi Arabia, and Pakistan.

The CIA and ISI-backed warlord proxies, such as Hekmatyar, Rabbani, and Sayyaf did not include any Durrani Pashtuns—the ethnic and tribal group with a royal ancestry, situated in their spiritual home of Kandahar and the southern provinces. The emergence of the Taliban in 1994 is connected directly to this sense of lost Pashtun royalty, as well as a reaction to the violent excesses of warlordism. Taliban can be translated as ‘students of Islam’ or ‘seekers of knowledge’, and were a part of traditional village life in Kandahar’s ‘Koran belt’. In 1996, led by Mullah Mohammed Omar, the Taliban swept to power on the back of promises to restore peace and Islamic values after decades of fighting. President Benazir Bhutto of Pakistan, together with the ISI and without the knowledge of Clinton, secretly supported the Taliban, sending fuel, machinery, and later money. In addition, Saudi Arabia sent funds through the ISI. The US tolerated the Taliban for most of the 1990s. Yet Osama bin Laden was now thoroughly ingratiated with Mullah Omar, as he launched a series of international terrorist attacks from Kandahar. There were now established links between the ISI, the Taliban, and al-Qaeda. Pakistan’s aim was to defeat Massoud’s Northern Alliance, who still clung to territory around the Panjshir valley; install a Pakistan-friendly government, and launch covert attacks against Indian forces in Kashmir. Despite the brutal record of the Taliban being well documented, and despite cracks in its governance spreading, the US—much to Massoud’s chagrin—was not interested in ‘interfering’ in Afghanistan, and the Taliban claimed Kandahar in 1994, Herat in 1995, and Kabul in 1996.

Against this backdrop, CIA operations in Afghanistan was subdued, as Clinton’s nominal isolationist foreign policy focused on state diplomacy and nuclear proliferation; its only involvement in Afghanistan was supporting the activity of American oil company Unocal, which had established links to the Taliban. It would take the terrorist attacks of September 11, 2001 to rekindle covert operations in the region. The Bush-Musharraf years cemented the historical pathways already trodden by the CIA and ISI, and repeated the same strategic mistakes. Neo-conservatives such as Dick Cheney, Paul Wolfowitz, and Donald Rumsfeld projected military power into Afghanistan, but ‘winning hearts and minds’ and ‘nation-building’ were off the table. Instead, the military and CIA sought security and control of the territory by lavishly funding warlords and drug barons with a billion-dollar budget, seeing this as a quick-fix that would free resources to channel to the war in Iraq. The State Department was sidelined by the Bush administration as the US military and the CIA became the de facto decision-makers in Afghanistan and Iraq. On the ground in Afghanistan, Special Operations Forces (SOF) led the attack against the Taliban, buoyed by soaring budgets. SOF would later become a cornerstone of strategy in Afghanistan, today involved in controversial ‘night-raids’. In sum, open democratic reform was once more overtaken by shadow wars that set the template for ‘drone diplomacy’, and solidified the patchwork of warlord fiefdoms that scarred the country.

Likewise, Pakistan. Gen. Mehmood Ahmad, director-general of the ISI, and one of the generals that put Musharraf in control, was virtually running the country’s foreign policy. A born-again Islamic fundamentalist, he supported the Taliban cause and Kashmiri militants. Pakistan’s military elite, which had ruled the country since independence in 1947, were in many ways a part of the security state bequeathed by the British state, and the landowning feudal class that underlined the system. Partition, the creation of Bangladesh, the constant insecurity of living next-door to a modernizing India (which Pakistan has repeatedly crossed swords with), motivated this elite to make ruinous domestic choices and sanction secretive violence in Kashmir, India, and Afghanistan. The ISI is the shadowy institution that in many ways embodies Pakistan’s identity crisis, which under Zia’s Islamist direction and the CIA’s funding, grew in influence throughout the 1980s. And Musharraf became the figurehead of this schizophrenia: touting modernization but supporting jihad.

The ISI supported (and continue to support) the Indian-hating Taliban, and switched its Kashmiri training camps to Afghanistan. But few in the Bush Administration saw this, or wanted to see it: Powell and Bush resisted criticizing Musharraf despite obvious links to the enemy they were fighting across the border. Pakistan was a vital asset to the US’ ‘Operation Enduring Freedom’, and on September 23, 2001, Bush waived all sanctions against Pakistan, in return for use of its facilities (CIA paramilitary teams and other special forces would be based at secret locations within Pakistan). In November 2001 Bush allowed hundreds of cornered Taliban and al-Qaeda leaders to be airlifted from Kunduz. One of the reasons this great escape was sanctioned by Bush and Cheney was that hundreds of ISI officers and soldiers from the Frontier Corp were among the Taliban. Indeed, the Taliban were quickly defeated in Afghanistan, but this exit was lined with dollars. According to Rashid (2008), the CIA had bought every Northern Alliance commander in sight and had bribed the Taliban commanders with a secret budget of $1 billion, legitimizing warlordism. ‘The irony was not lost on the Afghan people. Although the Americans had liberated them from the evil of the Taliban, they had brought back another evil: the warlords” (Rashid, 2008, p.131).

The CIA had incredible clout, virtually running the entire Afghan operation, including a network of secret prisons and black sites, and rendering ghost detainees around the world. Not only were they paying warlords with a billion-dollar budget, and granting them lucrative development contracts; by the summer of 2002, 45,000 Afghan mercenaries were on the CIA payroll and USAID humanitarian deliveries were being taken over by joint CIA-SOF teams. It would take Karzai’s central government to stem the power of warlords in Afghanistan, as mandated in the 2002 Bonn Agreement (and the widely hailed 2006 UN Program called Disarmament, Demobilization and Reintegration). But the CIA’s focus continued to be on the singular and elusive figure of Osama bin Laden, at the cost of wider development projects and reform. Peter Tomes, a former US ambassador to Afghanistan told Congress that CIA operations where the main hindrance to reconstruction and possessed too much money and power. “The real hindrance was still the CIA, which even in 2003 was deciding what projects other agencies should undertake on the basis of how those projects would affect the war on terrorism. USAID officials complained bitterly about CIA interference…” (Rashid, 2008, 185). Warlords, not the Afghan government, were empowered during this period, by drug money and by their CIA paymasters.

Across the border in Pakistan, the seeds were similarly been sown for further tragedy. In 2002 Musharraf engineered the success of Islamic extremist parties for his gain, in two key provinces bordering Afghanistan: NWFP and Balochistan. The MMA or United Council Action was a six-party alliance of Islamic fundamentalist parties, which contained the powerful Jamiat-Ulema-e-Islami, the party that was not only instrumental to the Taliban’s inception, but would support and provide refuge to fleeing fighters. The NWFP, in effect, became the state machinery for the Taliban. The ISI gave refuge to Hikmetyar, Jallaladin Haqqani, and the IMU—all of which settled in North and South Waziristan—places that would soon be visited by CIA Predator drones. As Rashid (2008) notes, US and NATO intelligence showed a systematic collusion between the ISI and the Taliban (and therefore, indirectly, al-Qaeda). Quetta was now the Taliban’s capital and the Federally Administered Tribal Areas (FATA) became the beating heart of militant activity in Central Asia—if not the world—and was the conduit for ISI support for the Taliban, just as it was the conduit for CIA and ISI support of the Afghan mujahideen only two decades earlier.

Thousands of Taliban and al-Qaeda settled in South and North Waziristan and restarted operations there, with Haqqani one of the key organizers, hiring tribesman to provide sanctuary and passage for jihadis: these same armed groups would later emerge as the ‘Pakistan Taliban’. “Confident of their safety, the Taliban and al Qaeda began to run their own fiefdom in South Waziristan, killing tribal elders considered to be spying on them for the Afghans or for the Americans and forcing others to flee with their families” (Rashid, 2008, p.269). FATA needed large-scale, structural development and political reform, but its status of a buffer state continued, and it was treated like an incorrigible warzone: with Pakistani military aggression followed by peace deals with the Taliban. All the while, tribal elders were executed and the population harassed. FATA was now the port of call for domestic and international terrorism.

For 30 years US and Pakistani administrations have secretly deployed their spy agencies in and around Afghanistan: with each other, in spite of each other, and because of each other. But each ‘victory’ was deferred into a greater tragedy: the mujahideen was a victory for ‘Cold War America’, but a tragedy for ‘War on Terror America’. The ISI’s sponsorship of the Taliban may have kept Indian influence at bay in Afghanistan, but the hundreds of madrassas now provide the ground for domestic terrorist activity that threatens to shred the very fabric of Pakistan’s national security. Contradiction after contradiction:  first as tragedy, then as farce.

Coll, S. 2004. Ghost Wars: The Secret History of the CIA, Afghanistan, and Bin Laden, from the Soviet Invasion to September 10, 2011.
Rashid, A. 2008. Descent into Chaos: Pakistan, Afghanistan, and the Threat to Global Security.
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