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The disembodied voice was chilling in its rage. A gunman, holed up in the Oberoi Trident hotel in Mumbai (formerly Bombay), where some 40 people had been taken hostage, told an Indian news channel that the attacks were revenge for the persecution of Muslims in India. "We love this as our country, but when our mothers and sisters were being killed, where was everybody?" he asked via telephone. No answer came. But then he probably wasn't expecting one.

The roots of Muslim rage run deep in India, nourished by a long-held sense of injustice over what many Indian Muslims believe is institutionalized discrimination against the country's largest minority group. The disparities between Muslims, who make up 13.4% of the population, and India's Hindus, who hover at around 80%, are striking. There are exceptions, of course, but generally speaking, Muslim Indians have shorter life spans, worse health, lower literacy levels and lower-paying jobs. Add to that toxic brew the lingering resentment over 2002's anti-Muslim riots in the state of Gujarat. The riots, instigated by Hindu nationalists, killed some 2,000 people, most of them Muslims. To this day, few of the perpetrators have been convicted. (See pictures of the terrorist shootings in Mumbai.)

The huge gap between Muslims and Hindus will continue to haunt India's — and neighboring Pakistan's — progress toward peace and prosperity. But before intercommunal relations can improve, there are even bigger problems that must first be worked out: the schism in subcontinental Islam and the religion's place and role in modern India and Pakistan. It is a crisis 150 years in the making.

The Beginning of the Problem
On the afternoon of March 29, 1857, Mangal Pandey, a handsome, mustachioed soldier in the East India Company's native regiment, attacked his British lieutenant. His hanging a week later sparked a subcontinental revolt known to Indians as the first war of independence and to the British as the Sepoy Mutiny. Retribution was swift, and though Pandey was a Hindu, it was the subcontinent's Muslims, whose Mughal King nominally held power in Delhi, who bore the brunt of British rage. The remnants of the Mughal Empire were dismantled, and 500 years of Muslim supremacy on the subcontinent came to a halt.

Muslim society in India collapsed. The British imposed English as the official language. The impact was cataclysmic. Muslims went from near 100% literacy to 20% within a half-century. The country's educated Muslim élite was effectively blocked from administrative jobs in the government. Between 1858 and 1878, only 57 out of 3,100 graduates of Calcutta University — then the center of South Asian education — were Muslims. While discrimination by both Hindus and the British played a role, it was as if the whole of Muslim society had retreated to lick its collective wounds.

Out of this period of introspection, two rival movements emerged to foster an Islamic ascendancy. Revivalist groups blamed the collapse of their empire on a society that had strayed too far from the teachings of the Koran. They promoted a return to a purer form of Islam, modeled on the life of the Prophet Muhammad. Others embraced the modern ways of their new rulers, seeking Muslim advancement through the pursuit of Western sciences, culture and law. From these movements two great Islamic institutions were born: Darul Uloom Deoband in northern India, rivaled only by Al Azhar University in Cairo for its teaching of Islam, and Aligarh Muslim University, a secular institution that promoted Muslim culture, philosophy and languages but left religion to the mosque. These two schools embody the fundamental split that continues to divide Islam in the subcontinent today. "You could say that Deoband and Aligarh are husband and wife, born from the same historical events," says Adil Siddiqui, information coordinator for Deoband. "But they live at daggers drawn."

The campus at Deoband is only a three-hour drive from New Delhi through the modern megasuburb of Noida. Strip malls and monster shopping complexes have consumed many of the mango groves that once framed the road to Deoband, but the contemporary world stops at the gate. The courtyards are packed with bearded young men wearing long, collared shirts and white caps. The air thrums with the voices of hundreds of students reciting the Koran from open-door classrooms.

Founded in 1866, the Deoband school quickly set itself apart from other traditional madrasahs, which were usually based in the home of the village mosque's prayer leader. Deoband's founders, a group of Muslim scholars from New Delhi, instituted a regimented system of classrooms, coursework, texts and exams. Instruction is in Urdu, Persian and Arabic, and the curriculum closely follows the teachings of the 18th century Indian Islamic scholar Mullah Nizamuddin Sehalvi. Graduates go on to study at Cairo's Al Azhar or the Islamic University of Medina in Saudi Arabia, or they found their own Deobandi institutions.

Today, more than 9,000 Deobandi madrasahs are scattered throughout India, Afghanistan and Pakistan, most infamously the Dara-ul-Uloom Haqaniya Akora Khattak, near Peshawar, Pakistan, where Mullah Mohammed Omar and several other leaders of Afghanistan's Taliban first tasted a life lived in accordance with Shari'a. Siddiqui visibly stiffens when those names are brought up. They have become synonymous with Islamic radicalism, and Siddiqui is careful to dissociate his institution from those who carry on its traditions, without actually condemning their actions. "Our books are being taught there," he says. "They have the same system and rules. But if someone is following the path of terrorism, it is because of local compulsions and local politics."

Sir Syed Ahmad Khan, who founded the Anglo-Mohammedan Oriental College at Aligarh in 1877, studied under the same teachers as the founders of Deoband. But he believed that the downfall of India's Muslims was due to their unwillingness to embrace modern ways. He decoupled religion from education and in his school sought to emulate the culture and training of India's new colonial masters. Islamic culture was part of the curriculum, but so were the latest advances in sciences, medicine and Western philosophy. The medium was English, the better to prepare students for civil-service jobs. He called his school the Oxford of the East. In architecture alone, the campus lives up to that name. A euphoric blend of clock towers, crenellated battlements, Mughal arches, domes and the staid red brick of Victorian institutions that only India's enthusiastic embrace of all things European could produce, the central campus of Aligarh today is haven to a diverse crowd of male and female, Hindu and Muslim students. Its law and medicine schools are among the top-ranked in India, but so are its arts faculty and Quranic Studies Centre. "With all this diversity, language, culture, secularism was the only way to go forward as a nation," says Aligarh's vice chancellor, P.K. Abdul Azis. "It was the new religion."

This fracture in religious doctrine — whether Islam should embrace the modern or revert to its fundamental origins — between two schools less than a day's donkey ride apart when they were founded, was barely remarked upon at the time. But over the course of the next 100 years, that tiny crack would split Islam into two warring ideologies with repercussions that reverberate around the world to this day. Before the split became a crisis, however, the founders of the Deoband and Aligarh universities shared the common goal of an independent India. Pedagogical leanings were overlooked as students and staff of both institutions joined with Hindus across the subcontinent to remove the yoke of colonial rule in the early decades of the 20th century.

Two Faiths, Two Nations
But nationalistic trends were pulling at the fragile alliance, and India began to splinter along ethnic and religious lines. Following World War I, a populist Muslim poet-philosopher by the name of Muhammad Iqbal framed the Islamic zeitgeist when he questioned the position of minority Muslims in a future, independent India. The solution, Iqbal proposed, was an independent state for Muslim-majority provinces in northwestern India, a separate country where Muslims would rule themselves. The idea of Pakistan was born.

Mohammed Ali Jinnah, the Savile Row–suited lawyer who midwifed Pakistan into existence on Aug. 14, 1947, was notoriously ambiguous about how he envisioned the country once it became an independent state. Both he and Iqbal, who were friends until the poet's death in 1938, had repeatedly stated their dream for a "modern, moderate and very enlightened Pakistan," says Sharifuddin Pirzada, Jinnah's personal secretary. Jinnah's own wish was that the Pakistani people, as members of a new, modern and democratic nation, would decide the country's direction.

But rarely in Pakistan's history have its people lived Jinnah's vision of a modern Muslim democracy. Only three times in its 62-year history has Pakistan seen a peaceful, democratic transition of power. With four disparate provinces, more than a dozen languages and dialects, and powerful neighbors, the country's leaders — be they Presidents, Prime Ministers or army chiefs — have been forced to knit the nation together with the only thing Pakistanis have in common: religion.

Following the 1971 civil war, when East Pakistan, now Bangladesh, broke away, the populist Prime Minister Zulfikar Ali Bhutto embarked on a Muslim-identity program to prevent the country from fracturing further. General Mohammed Zia ul-Haq continued the Islamization campaign when he overthrew Bhutto in 1977, hoping to garner favor with the religious parties, the only constituency available to a military dictator. He instituted Shari'a courts, made blasphemy illegal and established laws that punished fornicators with lashes and held that rape victims could be convicted of adultery. When the Soviet Union invaded neighboring Afghanistan in December 1979, Pakistan was already poised for its own Islamic revolution.

Almost overnight, thousands of refugees poured over the border into Pakistan. Camps mushroomed, and so did madrasahs. Ostensibly created to educate the refugees, they provided the ideal recruiting ground for a new breed of soldier: mujahedin, or holy warriors, trained to vanquish the infidel invaders in America's proxy war with the Soviet Union. Thousands of Pakistanis joined fellow Muslims from across the world to fight the Soviets. As far away as Karachi, high school kids started wearing "jihadi jackets," the pocketed vests popular with the mujahedin. Says Hamid Gul, then head of the Pakistan intelligence agency charged with arming and training the mujahedin: "In the 1980s, the world watched the people of Afghanistan stand up to tyranny, oppression and slavery. The spirit of jihad was rekindled, and it gave a new vision to the youth of Pakistan."

But jihad, as it is described in the Koran, does not end merely with political gain. It ends in a perfect Islamic state. The West's, and Pakistan's, cynical resurrection of something so profoundly powerful and complex unleashed a force that gave root to al-Qaeda's rage, the Taliban's dream of an Islamic utopia in Afghanistan, and in the dozens of radical Islamic groups rapidly replicating themselves in India and around the world today. "The promise of jihad was never fulfilled," says Gul. "Is it any wonder the fighting continues to this day?" Religion may have been used to unite Pakistan, but it is also tearing it apart.

India Today
In India, Islam is, in contrast, the other — purged by the British, denigrated by the Hindu right, mistrusted by the majority, marginalized by society. There are nearly as many Muslims in India as in all of Pakistan, but in a nation of more than a billion, they are still a minority, with all the burdens that minorities anywhere carry. Government surveys show that Muslims live shorter, poorer and unhealthier lives than Hindus and are often excluded from the better jobs. To be sure, there are Muslim success stories in the booming economy. Azim Premji, the founder of the outsourcing giant Wipro, is one of the richest individuals in India. But for many Muslims, the inequality of the boom has reinforced their exclusion.

Kashmir, a Muslim-dominated state whose fate had been left undecided in the chaos that led up to partition, remains a suppurating wound in India's Muslim psyche. As the cause of three wars between India and Pakistan — one of which nearly went nuclear in 1999 — Kashmir has become a symbol of profound injustice to Indian Muslims, who believe that their government cares little for Kashmir's claim of independence — which is based upon a 1948 U.N. resolution promising a plebiscite to determine the Kashmiri people's future. That frustration has spilled into the rest of India in the form of several devastating terrorist attacks that have made Indian Muslims both perpetrators and victims.

A mounting sense of persecution, fueled by the government's seeming reluctance to address the brutal anti-Muslim riots that killed more than 2,000 in the state of Gujarat in 2002, has aided the cause of homegrown militant groups. They include the banned Student Islamic Movement of India (SIMI), which was accused of detonating nine bombs in Mumbai during the course of 2003, killing close to 80. The 2006 terrorist attacks on the Mumbai commuter-rail system that killed 183 people were also blamed on SIMI as well as the pro-Kashmir Pakistani terrorist group Lashkar-e-Toiba (LeT). Those incidents exposed the all-too-common Hindu belief that Muslims aren't really Indian. "LeT, SIMI — it doesn't matter who was behind these attacks. They are all children of [Pervez] Musharraf," sneered Manish Shah, a Mumbai resident who lost his best friend in the explosions, referring to the then President of Pakistan. In India, unlike Pakistan, Islam does not unify but divide.

Still, many South Asian Muslims insist Islam is the one and only force that can bring the subcontinent together and return it to pre-eminence as a single whole. "We [Muslims] were the legal rulers of India, and in 1857 the British took that away from us," says Tarik Jan, a gentle-mannered scholar at Islamabad's Institute of Policy Studies. "In 1947 they should have given that back to the Muslims." Jan is no militant, but he pines for the golden era of the Mughal period in the 1700s and has a fervent desire to see India, Pakistan and Bangladesh reunited under Islamic rule.

That sense of injustice is at the root of Muslim identity today. It has permeated every aspect of society and forms the basis of rising Islamic radicalism on the subcontinent. "People are hungry for justice," says Ahmed Rashid, a Pakistani journalist and author of the new book Descent into Chaos. "It is perceived to be the fundamental promise of the Koran." These twin phenomena — the longing many Muslims feel to see their religion restored as the subcontinent's core, and the marks of both piety and extremism Islam bears — reflect the lack of strong political and civic institutions in the region for people to have faith in. If the subcontinent's governments can't provide those institutions, then terrorists like the Trident's mysterious caller will continue asking questions. And providing their own answers.

— With reporting by Jyoti Thottam / Mumbai and Ershad Mahmud / Islamabad