As a rule, the Muslims in India were poorer than the Hindus, as well as less educated. There were a few Muslim entrepreneurs, but no real Muslim middle class. They continued to be under-represented in the professions, and in government service. Forty per cent of Muslims in cities lived below the poverty line; the situation in the countryside was not much better.

The literacy rate for Muslims was well below the national average, and the gap between them and the other communities was growing. Few Muslim girls were sent to school, while the boys were often placed in madrasas (religious schools) whose archaic curricula did not equip them for jobs in the modern economy.

Meanwhile, the taunts of the Sangh Parivar had inculcated a defensive, almost siege mentality among the Muslim intelligentsia. The young men, especially, sought succour in religion, seeing in a renewed commitment to Islam an alternative to poverty and persecution in the world outside. Nor was this turn to faith always quietist. A Students Islamic Movement of India had arisen, whose leaders argued that threats from the rival religion could be met only through force of arms.

The rise of Hindu fundamentalism in the 1990s put an already vulnerable minority further on the defensive. In the border state of Jammu and Kashmir, however, the roles were reversed. Here, the Muslim majority was increasingly expressing its aspirations in religious terms, with the Hindu minority suffering as a consequence.

The popular revolt that broke out in the Valley in 1989 was at first led by the Jammu and Kashmir Liberation Front. Within a year, however, the JKLF had ceded ground to the Hizb-ul Mujahideen, whose own commitment to a multireligious Kashmir was much less certain. The cry of azaadi (freedom) was being replaced by the call of jihad (holy war). As a popular slogan of the Hizb-ul cadres went: “Na guerrilla jang, na qaumi jang: al jihad, al jihad.” (This is neither a guerrilla war nor a national liberation struggle; this is jihad, jihad.)

One consequence of this turn to religion was that the community of Kashmiri Pandits became suspect in the eyes of the militants. They were Hindus, but in other respects akin to their Muslim brethren, speaking the same language, eating the same kind of food, partaking of the same syncretic culture of the Valley.

In the past there had been economic rivalry between Hindus and Muslims. Sheikh Abdullah, for example, had resented and then brought to an end Pandit control of cultivable land and of the state administration. But the social harmony was more or less complete. Even in the Partition riots of 1947 Kashmir was untouched, an oasis of peace lauded by Mahatma Gandhi himself.

In the winter of 1989-90, as the Hizb-ul supplanted the JKLF, the Pandits became a target of attack. Because they were Hindus, and for no other reason, they were seen as agents of a state that had for so long oppressed the Kashmiris. Several hundred Pandits were killed in 1989–90, and killed in ways that made the ones who survived deeply insecure. As a reporter who documented these murders later wrote:

These women and men were not killed in the cross-fire, accidentally, but were systematically and brutally targeted. Many of the women were gang-raped before they were killed. One woman was bisected by a mill saw. The bodies of the men bore marks of torture. Death by strangulation, hanging, amputations, the gouging out of eyes, were not uncommon. Often their bodies were dumped with notes forbidding anyone – on pain of death – to touch them.

In panic, Pandit families began leaving the Valley for the Hindu-majority Jammu region. Others fled further afield, to Delhi and even to Bombay. There were an estimated 200,000 Pandits living in the Kashmir Valley. By the summer of 1990, at least half had left. They lived in refugee camps, some run by the government, others by the RSS. At first the state’s hope, and their own, was that the migration was temporary, and that once peace returned to the Valley then so would they. In the event, they stayed on, and on.

Throughout the 1990s there were further attacks on Pandits who had chosen to remain. Sometimes entire hamlets were set on fire. By the end of the decade, fewer than 4,000 Pandits were left in the Valley, a melancholy reminder of the centuries in which they had lived cheek-by-jowl with their compatriots.

The growing militancy in Kashmir was actively aided by Pakistan. That country’s Inter-Services Intelligence (ISI) ran camps where terrorists were trained in the use of arms and provided maps of the region. With the ISI’s help, Kashmiri activists moved freely across the border, into India to kill or bomb, then back to Pakistan for rest and replenishment. By now, indigenous militants had been joined by foreign mercenaries – Arabs, Chechens, Uzbeks – who had cut their teeth in the war against the Soviet puppet regime in Afghanistan. When that war ended, and Russian troops had returned, defeated, to their homeland, these fighters found another holy cause in the liberation of Kashmir.

By the mid 1990s the Hizb-ul had been joined by many hundreds of mehmani mujahideen (guest freedom-fighters). These owed allegiance to different groups, all of which were headquartered in Pakistan, and all of which practised the austere, fundamentalist version of Islam taught in that country’s many religious schools. Through the 1980s, the Islamicisation of Pakistani society had proceeded apace.

At the nation’s birth in 1947 it had a mere 136 madrasas; by 2000 it had as many as 30,000. These madrasas, writes Tariq Ali, were “indoctrination nurseries designed to produce fanatics”. Pakistan now boasted fifty-eight Islamic political parties and twenty-four armed religious militias, peopled in the main by the products of the madrasa system.

The intensification of religious sentiment in Pakistan deepened its commitment to the “liberation” of Kashmir. Preachers in mosques and madrasas spoke repeatedly of Indian zulm (terror) in the Kashmir Valley, urging their followers to join the jihad there. Youths so swayed entered groups such as the Lashkar-i-Toiba, which was rapidly assuming a leading role in the armed struggle.

The proximate aim was the uniting of Kashmir with the Pakistani nation, this “a religious duty binding not only on the people of Pakistan, but, in fact, on the entire Muslim ummat [brotherhood]”. A wider ambition was to catalyse a civil war in India. As the chief of the Lashkar, Hafiz Mohammed Saeed, boasted, they were aiming to “set up a mujahideen network across India”, which, when it was up and running, would spell “the start of the disintegration of India”.

“Revenge is our religious duty,” said Saeed to an American journalist. “We beat the Russian superpower in Afghanistan; we can beat the Indian forces too. We fight with the help of Allah, and once we start jehad, no force can withstand us.” Speaking to a Pakistani reporter, the Lashkar chief claimed that “our struggle will continue even if Kashmir is liberated. We still have to take revenge [against India] for [the loss of] East Pakistan.”

This animosity and hatred was perhaps not unexpected. For the jihadis, India was the land of the kafirs, or unbelievers. But as it happened their wrath was being visited on some co-religionists as well. There were killings of activists from the National Conference, which wanted autonomy within India, of the JKLF, which wanted independence rather than merger with Pakistan, and of the People’s Conference, which advocated non-violence.

The fundamentalists also came down hard on the pleasures of the people. Cinema halls and video parlours were closed, and drinking and smoking banned. Militant groups distributed leaflets ordering women to cover themselves from head to toe by wearing the long black veil, or burqa. The burqa was contrary to Kashmiri custom – here many women did not even wear headscarves. Besides, they cost Rs 2,000 apiece. Cynics suggested that tailors and cloth merchants were behind the move. There were, withal, savage attempts to enforce the ban, with acid being thrown on women who disregarded it.

The main target of fundamentalist ire, however, was the Indian state and its symbols. Scarcely a week passed without a suicide attack on an army post or police camp, to stop or stem which even more troops were moved into the Valley. There were now bunkers on every street corner in Srinagar.

The Indian army had become “an imposing and ubiquitous presence” in Kashmir, a “parallel government” even. It was charged not merely with the maintenance of law and order, but also with running hospitals, airports, bus stations and tourist centres. The state government had abdicated most of its duties. By 1995 or thereabouts, there were only two functioning institutions in Kashmir – the Indian army on the one side and the network of jihadi groups on the other.

As the Valley came to resemble a zone of occupation, popular sentiment rallied to the jihadi cause. Terrorists mingled easily with the locals, and were given refuge before or after their actions. When their men were killed in bomb attacks, the reprisals of the Indian security forces could be murderous. Soldiers dropped in unannounced in remote villages, searching for terrorists – when they did not find them, they beat up the peasants instead. A large number of custodial deaths were also reported.

The costs of this apparently unending war were colossal. According to government figures, between January 1990 and August 2001 some 12,000 civilians died unnatural deaths – three-quarters at the hands of militants, the rest in the cross-fire. Security forces claimed to have killed 13,400 militants, while losing 3,100 of their own.

Given the low population densities, so many deaths in Kashmir was the equivalent of 4 million Indians being killed in the country as a whole. The casualties were spread all across this lovely if increasingly desolate Valley. However, they were mostly of young men, of Kashmiris who came of age in this cursed decade. The journalist Muzamil Jaleel, who almost became a militant himself, later visited a graveyard near his native village, where he found twenty-one tombstones recording the deaths of his friends and classmates.

As James Buchan has written, in the years since 1990, the Kashmiri Muslims and the Indian government conspired to abolish the complexities of Kashmiri civilisation. The world [it] inhabited has vanished: the state government and the political class, the rule of law, almost all the…Hindu inhabitants of the valley, alcohol, cinemas, cricket matches, picnics by moonlight in the saffron fields, schools, universities, an independent press, tourists and…banks. In this reduction of civilian reality, the sights of Kashmir…are redefined: not the…lakes and Mogul gardens…or the storied triumphs of Kashmiri agriculture, handicrafts and cookery, but two entities that confront each other without intermediary: the mosque and the army camp.

Throughout the 1990s, as Hindu fundamentalism gathered strength in the rest of India, Islamic fundamentalism was on the ascendant in Kashmir. The two processes began independently, yet each legitimised and furthered the other.

With every communal riot sparked by the Ayodhya movement, radicals in the Valley could more easily portray India as a state run for and by Hindus. With every killing of innocent civilians or Indian soldiers in the Valley, the RSS could point to the hand of Pakistan in fomenting trouble within India.

There were two critical events that, as it were, defined this epoch of competitive fundamentalisms: the destruction of the Babri Masjid and the exodus of the Kashmiri Pandits. Would one trust a state that could not honour its commitment to protect an ancient place of worship? Would one trust a community that so brutally expelled those of a different faith? Such questions resonated across the subcontinent, asked by countless Indians not previously known to think along lines of religion and faith.

Excerpted with permission from India After Gandhi: The History of the World’s Largest Democracy, Ramachandra Guha, Picador, Pan Macmillan India.