Ultimately, Pakistani leaders are more worried about domestic backlash than U.S. threats, so any U.S. effort to stabilize Afghanistan will find that Pakistan continues to be a problematic partner.

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Pakistan has long been a complicated counterterrorism partner

U.S. frustration with Pakistan goes back to the 1990s, when Pakistan supported Islamist militants in India-held Kashmir — and saw these groups as important allies in the country’s struggle with India. Pakistan also supported the Taliban in the 1990s, looking to exert influence over Afghanistan. The United States, by contrast, saw both Kashmiri militants and the al-Qaeda-supporting Taliban as terrorists. U.S. criticism at the time — and Pakistani foot-dragging — led to considerable tensions in the bilateral relationship.

After the 9/11 terrorist attacks, Pakistan proved to be an important, but still frustrating, counterterrorism partner. Pakistani military ruler Pervez Musharraf cut off ties with the Taliban, cooperated with the U.S. invasion and arrested numerous al-Qaeda members in the country. But he allowed many Kashmiri militant groups to keep operating. Additionally, the military and Pakistan’s powerful intelligence agency — the Inter-Services Intelligence — maintained ties with Afghan militants. This includes the notorious Haqqani network, a group affiliated with the Taliban that has launched brutal attacks against U.S. and Afghan forces.

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Pakistan also failed to control its border with Afghanistan, which allowed militants to escape the U.S. military. This unstable situation continued after Musharraf stepped down in 2008 and a series of civilian leaders replaced him. For example, in 2011, Adm. Mike Mullen — the top U.S. military official — claimed that Pakistan’s intelligence agency supported an attack by the Haqqani network against the U.S. Embassy in Afghanistan.

Pakistan’s politics and religion have been closely linked for decades

The situation in Pakistan reflects the inertia of a decades-long intertwining of Pakistan’s security and Islamic politics.

Muhammad Ali Jinnah, an Indian politician, pushed for the founding of Pakistan as a country for South Asia’s Muslims (rather than an expressly Islamic state) during the negotiations for India’s independence in 1947. Yet as Pakistani journalist Abbas Nasir recently wrote, the Objectives Resolution — presented by Jinnah’s successor — changed this. This document established Islam as the official religion of Pakistan and the basis for its laws. At the same time, the Pakistani military justified its power by pointing to the threat from India and — according to Pakistan expert Christine Fair — the need to defend Islam.

Islam became more intertwined with Pakistan’s security in the 1960s and 1970s. As historian Husain Haqqani discusses, when East Pakistan — later Bangladesh — pushed for autonomy in the late 1960s, Pakistani military leaders turned to Islamists to terrorize pro-secession forces. In the 1970s, socialist Prime Minister Zulfiqar Ali Bhutto called Pakistan’s nuclear weapons efforts a struggle for an “Islamic bomb.”

Military ruler Mohammed Zia ul-Haq overthrew Bhutto in 1977, then worked with the United States and Saudi Arabia to support the mujahideen, or fighters, resisting the Soviet invasion of neighboring Afghanistan. Islamist organizations that were part of the fight, including al-Qaeda, established connections in Pakistan that lasted beyond the Soviet withdrawal. Zia also implemented a domestic “Islamization” program, expanding conservative Islamic laws in the country.

Pakistan’s leaders found it difficult to change course

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By the 1990s, the Pakistani military was committed to continuing its support for militants, and powerful Islamist groups loudly protested any attempt at change. A series of weak civilian leaders continued Zia’s policies by default. As Prime Minister Benazir Bhutto described her policies on the Taliban in the mid-1990s (as quoted in Steve Coll’s “Ghost Wars“), Pakistan’s leaders were “slowly sucked into” continued support and enabling of militants.

This is what led to the situation the United States now faces. After 9/11, Musharraf faced a domestic backlash over his crackdown on al-Qaeda and other groups, as critics saw this as betraying Pakistan’s ideals. As I discuss in my book, one editorial attacking Musharraf even said jihad “is not only a basic concept of Islam” but also “part of the Pakistani Army motto since independence.”

Reluctant to provoke too much anger, Musharraf moderated his cooperation with the U.S. effort in Afghanistan. His civilian successors were similarly attacked for any tough counterterrorism policies. They, too, avoided controversial steps, such as cutting ties with the Haqqani network.

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Thus, Pakistan’s current hesitation to crack down on militant groups is not because Pakistani leaders sympathize with al-Qaeda or reject U.S. leadership. Instead, these early connections between Islam and the country’s security set a precedent for later appeals to Islam by Pakistani leaders.

And government support for militants in Kashmir and elsewhere led powerful Islamist groups to back Pakistan’s security policies, but also gave militant groups and their supporters extra sway over politics. Leaders who were unhappy with this arrangement found themselves facing intense pressure from society and the military when they tried to change this situation.

What this means for Trump’s Afghanistan strategy

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If Pakistan had a conscious policy of allowing a “haven for terrorists” in its territory, U.S. pressure might persuade the leadership to change it. Because the current situation reflects complicated domestic politics and any shift would probably result in pushback from the powerful military, the changes Washington wants are not likely to happen.

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The United States has been putting pressure on Pakistan for decades, and neither tough words nor threats to cut off aid have worked for long. That suggests Pakistani leaders appear more afraid of a backlash from their society and military than they are of U.S. anger.

This does not bode well for the Trump administration’s new Afghanistan strategy. Stabilizing Afghanistan will be much easier with a cooperative Pakistan, but that is unlikely to happen. Instead of making threats, U.S. policymakers would be better off working out whatever temporary arrangements they can with Pakistan, realizing the constraints of Pakistan’s leaders — and perhaps considering other options that do not rely on Pakistan.