Pakistan’s Birth Defect: How a State Built on Islamist Supremacy Became the World’s Most Enduring Incubator of Jihadism

By Najeeb Kakar

Quisling-I-Azam? Pakistan founder Muhammad Ali Jinnah with Lord Mountbatten.

For decades, global policymakers have searched for the ideological roots of modern jihadism. They have focused on Saudi Arabia’s Wahhabism, Iran’s clerical revolution, and the post war chaos in Afghanistan. Yet they often overlook the most consequential incubator of all. The most durable and state engineered jihadist mindset in today’s Muslim world did not originate in Riyadh or Qom. It emerged in Pakistan.

This is not a condemnation of ordinary Pakistanis. It is an indictment of an ideology that became national doctrine. Pakistan is the only major state whose very conception and political identity were built on an explicitly communal theory that treated Muslim supremacy as the foundation of nationhood. That project long predates General Zia ul Haq. His regime did not invent the idea. It only militarised and globalised it.

The result is a state that has repeatedly produced jihadist militancy, exported it across borders, and then demanded Western support as a “frontline ally” against the very forces it helped create.

An Ideology Older Than the State

The story does not begin in 1979. It begins with the first Partition of Bengal in 1905 and the politics that followed. British colonial policies, separate electorates, and elite Muslim anxieties about majority rule encouraged a new kind of communal mobilisation. In 1906, the All India Muslim League was formed in Dacca by Muslim notables who claimed to represent a distinct “Muslim community” with separate political interests inside British India.

Over the next decades, this political project hardened into the Two Nation Theory. According to this doctrine, Hindus and Muslims were not just religious communities within one civilisation, they were separate nations that could not live together in a democratic order. The fear was not genocide or apartheid. It was loss of elite dominance. Muslim political elites, long accustomed to influence under the Mughal and other Muslim dynasties, feared marginalisation in a future democratic India where Hindus would be the majority.

The demand for Pakistan was therefore not a demand for ethnic self determination. There is no ethnic group called “Pak.” Unlike Afghanistan, which literally means “land of the Afghans,” or Uzbekistan, which means “land of the Uzbeks,” Pakistan was conceived as an ideological territory.

Choudhry Rahmat Ali’s 1933 pamphlet Now or Never, often called the Pakistan Declaration, coined the name “Pakstan,” which carried a deliberate double meaning. It was partly an acronym of regions, but also literally the “Land of the Pure,” since “pak” in Persian and Urdu means “pure.”

From that point onward, the idea of Pakistan fused political separatism with a moral hierarchy. The “land of the pure” implied that those outside this ideological project were impure. Later, as Farahnaz Ispahani has shown in Purifying the Land of the Pure, the state would use this conception to marginalise and expel religious minorities in the name of purifying the body politic.

In other words, the soil for an exclusivist, quasi jihadist worldview was being prepared decades before Zia. The elite consensus that Muslims must rule themselves separately and that non Muslim presence diluted the purity of the community is not a side note. It is the foundation.

From Political Supremacy to Theological Absolutism

By the mid twentieth century, this political project intersected with Islamist thinkers who wanted not only a separate Muslim state, but a full Islamic order. Abul Ala Maududi, founder of Jamaat e Islami in British India and later Pakistan, argued that Muslims had an obligation to establish an Islamic state based on sharia and that the world was divided into a House of Islam and a House of War.

In his book Chasing a Mirage: The Tragic Illusion of an Islamic State, the late Toronto based journalist and writer Tarek Fatah devoted an entire chapter to “Pakistan, failure of an Islamic state.” He traced how Maududi’s ideas, combined with the Two Nation Theory, turned Pakistan into a laboratory for the Islamist dream of a sharia state and for a politics that normalised perpetual jihad as a tool of policy.

Long before the Soviet invasion of Afghanistan, Pakistan’s establishment had already used militant religious rhetoric and irregular fighters in Kashmir in 1947–48. It backed tribal militias and volunteers in the name of jihad to seize territory from India at independence. This pattern continued with episodic support to Islamist and separatist groups in the region.

Zia ul Haq did not invent this logic. He inherited a state already conceived as a religiously defined fortress and a political culture accustomed to using faith as a weapon.

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A State Founded on Supremacy, Not Territory

When Pakistan finally emerged in 1947, the Two Nation Theory became state doctrine. The new country was not an ethnic homeland in the modern sense. It was a political entity justified by a belief that Muslims could not safely or honourably live under the rule of a non Muslim majority.

That belief carried several implications.

First, it meant that equality inside a democratic India was not enough. Coexistence itself was defined as unacceptable. As one recent analysis of the Two Nation Theory notes, the doctrine was “a political power grab dressed in supremacist clothing,” built on the assertion that Muslims could not share power, culture, or space with others.

Second, it made it easier to present non Muslims and even “less pure” Muslims as internal threats. This logic would later be turned against Ahmadis, Shia, and smaller sects, and was used to delegitimise Bengali Muslims in what became Bangladesh, who were often portrayed as insufficiently pure or loyal to the central state.

Third, it created a permanent sense of siege that could justify endless mobilisation. Pakistan’s military and intelligence elites did not see themselves as managing a normal nation state. They saw themselves as guardians of an ideological frontier against India, against secularism, and later against any internal dissent that challenged their version of Islam.

Zia ul Haq: From Ideological State to Jihadist State

If the early decades of Pakistan laid the ideological foundation, General Zia ul Haq constructed the operational architecture of modern jihad. He seized power in 1977, Islamised the constitution and legal system, and aligned the state with Saudi funded Salafi and Wahhabi currents that were far more rigid than Pakistan’s traditional Islamic practice.

The Soviet invasion of Afghanistan in 1979 gave him the perfect opportunity. As scholars like Husain Haqqani have documented in Pakistan: Between Mosque and Military, Zia transformed Pakistan into the logistical hub and ideological engine of the Afghan jihad. The Inter Services Intelligence Directorate coordinated funding, training, and arming of mujahideen fighters from across the Muslim world.

Saudi Arabia poured in petrodollars, American and Western intelligence agencies supplied weapons and training, and Pakistani state media glorified jihad as a national duty. One analysis of the Islamisation period notes that under Zia “Pakistani style jihadist Islam” emerged, turning jihad from a largely defensive concept into an offensive doctrine and spawning a full generation of militants.

The earlier ideological claim that Muslims must rule themselves separately now fused with a global militant project. Jihad was no longer simply a rhetorical tool. It became institutionalised as foreign policy.

Pakistan as the Epicentre of Global Jihad

By the late twentieth century, Pakistan had become what multiple analysts bluntly describe as a global hub of jihadist militancy.

• A study of madrassas and militancy notes that Pakistan hosted dozens of militant organisations and that a significant share of known terrorists linked to global jihadist terrorism had passed through its networks or training environments.

• An International Crisis Group report titled Pakistan: The Militant Jihadi Challenge details how militant groups rooted in Pakistan operate across Punjab, the former FATA, Khyber Pakhtunkhwa, and Kashmir, with deep ties to the state’s security establishment.

• Counterterrorism analysts such as Rohan Gunaratna have traced how Al Qaeda and related networks used Pakistan’s tribal areas and Pakistani jihadist groups as training and staging grounds for attacks worldwide.

• A study on Global Jihad and America concludes that “Afghanistan and Pakistan will remain the epicenter of global jihad for an indefinite period,” reflecting the long term structural role that Pakistan plays in this ecosystem.

Husain Haqqani has described Pakistan’s security establishment as running a “jihad factory,” using militant groups as instruments of policy from Afghanistan to Kashmir.

Your late friend, Tarek Fatah, repeatedly warned that Pakistan exemplified “the tragic illusion of an Islamic state,” where the pursuit of religious purity and political Islam produced a permanent cycle of violence that threatened not only neighbours and the West, but especially liberal and secular Muslims.

A State that Profits from Extremism While Exporting the Costs

Pakistan gained enormously from this system.

It received billions in military and economic aid during the anti Soviet jihad, then again after 2001 as a supposed ally against terrorism. It built one of the largest militaries in the Muslim world. It acquired nuclear weapons and marketed them as an “Islamic bomb,” unique among Muslim majority states.

At the same time, it used jihadist proxies to shape Afghanistan, pressure India, suppress ethnic movements in Balochistan and elsewhere, and intimidate political opponents at home. When any group became too costly, Islamabad tried to rebrand or reorganise it rather than dismantle the underlying infrastructure.

The result is a system in which the state has repeatedly treated jihadist groups as adjustable tools, while insisting to the outside world that it is a victim and a partner in counterterrorism.

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The Taliban Reversal and Pakistan’s Strategic Shock

When the United States withdrew from Afghanistan, Pakistan’s political and military leaders framed it openly as a strategic victory. Commentators, ministers, and retired generals celebrated the “defeat of another superpower” and assumed that the Taliban would once again act as a pliable proxy deliver strategic depth, and help extend Pakistan’s ideological reach into Central Asia and toward India.

Instead, the Taliban began to chart a more independent course. They engaged with China, Iran, Russia, and Central Asian governments. They refused to act as Pakistan’s enforcers against the Pakistani Taliban, who continue to attack Pakistani security forces.

The sponsor found itself undermined by its own former clients. Pakistan, which had imagined itself using the Taliban to advance its regional fantasies, discovered that the Taliban were now using Pakistan for their own leverage.

This strategic shock has revived old habits in Islamabad. Under pressure from a resurgent domestic insurgency and economic crisis, sections of the establishment are again exploring new proxies and leverage inside Afghanistan, rather than abandoning the jihadist playbook.

Why the West Still Misreads Pakistan

Despite all this, many Western governments still misread Pakistan. They view the country through a narrow lens, as either a troubled ally, a nuclear power that must be managed, or a logistical corridor to Afghanistan. Each time there is a crisis, they return to Islamabad, hoping to use Pakistan to stabilise the region.

In doing so, they risk repeating the same error that defined the Cold War. Pakistan has consistently used Western fears and strategic needs to secure money, weapons, and legitimacy, while continuing to nurture and protect key elements of the jihadist ecosystem.

The problem is not incidental. It is structural. It flows from the country’s founding logic, from the belief that it is a fortress of the pure in a hostile environment and that religious mobilisation and armed non state actors are legitimate tools of policy.

The Core Truth the World Needs to Face

Pakistan is not the only country where extremist movements exist. It is unique in three critical ways.

1. Founding Ideology

   It is one of the very few modern states created explicitly on a religious communal theory, rather than on civic or ethnic nationhood. The Two Nation Theory and the symbolism of the “Land of the Pure” make religious supremacy a core part of the national story, not a later deviation.

2. State Jihad Infrastructure

   It has built, over several decades, a sophisticated infrastructure of training camps, indoctrination networks, and proxy organisations that have operated across Afghanistan, India, and beyond. This is not merely toleration of extremism. It is active cultivation.

3. Nuclear Shield

   It is the only Muslim majority state with a declared nuclear arsenal, which gives its establishment a sense of impunity and complicates international responses to its sponsorship of militant groups.

This combination makes Pakistan the most dangerous incubator of jihadist ideology on the planet. Not because its people are uniquely extreme, but because its state was built on a supremacist religious logic and then structured its security doctrine around the permanent use of religiously framed militancy.

If the international community is serious about confronting global jihad, stabilising South Asia, and protecting pluralism, it must finally confront this uncomfortable reality. Afghanistan, the Middle East, and Western cities may be the visible battlefields, but the intellectual, organisational, and strategic heart of many of these movements has long pulsed in Pakistan.

The most dangerous jihadist mindset in the Islamic world did not suddenly appear in the 1980s under Zia. It was seeded in the early twentieth century, nurtured through partition, embedded in state ideology at independence, and only then weaponised with Cold War money.

Until that deeper story is understood and addressed, Pakistan will remain the world’s most enduring incubator of militant extremism.

*Pashtun patriot Najeeb Kakar is an economist, human rights defender and political analyst, and an adjunct professor. He is an alumnus of the State University of New York (University at Albany). He writes on geopolitics and economic policy of southwest Asia. Follow on X: @Najeebkakar_1

The article was originally published as a guest post on Ahmar Mustikhan's Baloch spring.

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