Each regime that came into power sought to legitimize itself through an explicit ideology: The Ayub regime propounded the philosophy of modernization and economic development. The Bhutto regime donned the mantle of redeeming the poor through socialism. Zia having come into power through a coup d'etat, sought to perpetuate military rule through the garb of a coercive and obscurantist version of Islamic ideology.

In the absence of popular legitimacy, the Zia regime used terror for the first time in Pakistan's history as a conscious policy of the government. President Zia ul Haq publicly stated: "Martial law should be based on fear". In the same vein, Brigadier Malik wrote: "Terror struck into the hearts of enemies is not only a means, it is the end itself". (Quoted in Omar Noman's book: The Political Economy of Pakistan). In the pursuit of this policy, the democratic constitution of 1973 was set aside and draconian measures of military courts, arbitrary arrests, amputation of hands and public lashing were introduced.

Pakistan's society, by and large, was historically characterized by cultural diversity, democratic aspirations and a religious perspective rooted in tolerance and humanism. This was one of the reasons why the founding father, Quaid-e-Azam Muhammad Ali Jinnah conceived of Pakistan's polity as democratic and pluralistic with religious belief to be a matter concerning the individual rather than the state.

"You may belong to any religion or caste or creed ___ that has nothing to do with the business of the state….. We are starting with this fundamental principle that we are all citizens and equal citizens of one state…. Now, I think we should keep that in front of us as our ideal and you will find that in the course of time Hindus would cease to be Hindus and Muslims would cease to be Muslims, not in the religious sense, because that is the personal faith of each individual but in the political sense as citizens of the state."

President Zia-ul-Haq in attempting to restructure such a state and society into a theocracy, undertook two kinds of initiatives: First, measures designed to subordinate to executive authority, institutions of state and civil society such as the judiciary and the press, which if allowed to function independently could check governmental power. In the case of the judiciary its essential powers to scrutinize the legality of martial law or the orders of military courts were abolished. The judicial protection against arbitrary detention of a citizen embodied in the right to Habeas Corpus was eliminated for the first time in Pakistan.

In the case of the press, President Zia ul Haq gave a pithy statement of Martial Law Policy with respect to the press: "Democracy means freedom of the press, Martial Law its very negation". In the pursuit of this policy, press control measures were introduced. The government constituted committees at the district level to ensure that articles repugnant to the ideology of Pakistan were not published. Those members of the press who had refused to acquiesce faced state repression. A number of newspapers were banned and journalists were arrested and given flogging sentences by military courts.

The second set of measures towards a theocratic state sought to inculcate obscurantist views and induced a narrowing of the citizens mind. It involved a suspension of the sensibility of love and reason underlying the religious tradition embodied in Pakistan's folk culture.

In the absence of a popular mandate, Zia claimed that his mission to bring an "Islamic Order" in Pakistan had a divine sanction: "I have a mission given by God to bring Islamic Order to Pakistan". Advocacy for a theocratic social order was conducted through the state controlled television and press. Furthermore the State undertook to physically intervene in controlling individual behaviour with respect to the practice of religion. In August 1984 for example, the Nizam-e-Salat Campaign was launched through the appointment of 100,000 "Prayer Wardens" for rural and urban localities. The task of these state functionaries was to monitor religious activities of individuals and to seek their compliance in religious practices.

The institutional roots of "Islamic Fundamentalism" were laid when government funds were provided for establishing mosque schools (madrassas) in small towns and rural areas which led to the rapid growth of militant religious organisations. This social process which later came to be known as "Islamic Fundamentalism" was catalyzed by the Afghan war.

As General Zia moved towards the construction of a theocratic state and brutalized civil society, his isolation from the people as a whole was matched by increased external support. He sought political, economic and military support from the U.S. by offering to play the role of a front line state in the Afghan guerilla war against the occupying Soviet army. Accordingly, Pakistan obtained a package of U.S. $ 3.2 billion in financial loans and relatively sophisticated military hardware. Moreover, with support from the U.S., Pakistan was able to get additional fiscal space by getting its foreign debt rescheduled, and getting increased private foreign capital inflows. These official and private capital inflows played an important role in stimulating macro economic growth in this period. For example GDP growth rate increased from 5% per annum during the Bhutto regime to 6.6% per annum during the Zia regime. Foreign capital inflows also helped establish a political constituency both within the institutions of the state and in the conservative sections of the urban middle classes, for a theocratic form of military dictatorship.

As the Zia regime engaged in a proxy war, some of the militant religious groups together with their associated madrassas were provided with official funds, training and weapons to conduct guerilla operations in Afghanistan. While they helped fight the war in Afghanistan, the religious militant groups were able to enlarge the political space within Pakistan's society and some of the institutions of the State.

From 1987 onwards, sectarian violence mushroomed in the Punjab province (which till then had been relatively peaceful) and later spread across the country. The phenomenon of large scale sectarian violence conducted by well armed and trained cadres was closely associated with the rapid growth of Deeni Madrassas ("religious" schools). Historically, such schools basically imparted religious knowledge. In the late 1980s however a new kind of Deeni Madrassa emerged, which engaged in systematic indoctrination in a narrow sectarian identity, and inculcated hatred and violence against other sects. In 1998 there were 3,393 Deeni Madrassas in the Punjab alone and 67% had emerged during the period of the Zia regime and after. Between 1979 and 1994, many of the madrassas were receiving financial grants from Zakat funds. According to an official report of the police department, most of the madrassas were in fact providing religious education. Yet as many as 42% of them were actively promoting sectarian violence through a well conceived indoctrination process. The students predominantly from poor families were given free food and lodging during their term at the madrassas. As poverty increased in the 1990s, the burgeoning madrassas provided a growing number of unemployed and impoverished youths with the security of food, shelter and an emotionally charged identity: a personality that felt fulfilled through violence against the other.

As the new kind of sectarian madrassas emerged and grew during the Zia regime so did sectarian violence. The number of sectarian killings increased from 22 during the 1987-89 period, to 166 during the 1993-95 period. Thus violence against the other became both the expression and the emblem of the narrowed identity.

The mobilisation of these narrow identities involved a psychic disconnection from the well springs of universal human brotherhood within the Islamic tradition. Its liberating elements of rationality and love, were replaced in the narrowed psyche, by bigotry and hatred. Violence against the "other" became an emblem of membership within these identities. Thus, civil society divorced from its universal human values began to lose its cohesion and stability.