WASHINGTON—Hardly a day goes by without news about the penetration of the Pakistani state by Islamic fanaticism and the connection between that country’s Inter-Services Intelligence directorate and radical groups in Afghanistan, including the Taliban.

Fortunately for those who want to better understand Pakistan—the main theater of war for Asia and the Middle East today—a documentary on Benazir Bhutto, the former prime minister assassinated soon after returning from exile in the waning days of dictator Pervez Musharraf’s regime, has been released in the United States. “Bhutto,” directed by Duane Baughman and Johnny O’Hara, is generally laudatory, though enough information is given about the murder of Murtaza Bhutto, Benazir’s estranged brother and rival, which Murtaza’s daughter blames on Benazir, and the allegations of corruption against current President Asif Ali Zardari, Benazir’s husband who spent eight years in jail but was not charged, for viewers to be left wondering.

By far the most important contribution of the film, however, is something that does not constitute its primary focus—the gradual pervasiveness of religious fanaticism throughout Pakistan’s institutions and society since the 1980s.

Benazir’s father, Zulfiqar Ali Bhutto, the first civilian head of state after the civil war that led to Bangladesh’s separation from Pakistan in 1971, moderately encouraged Islam as a nationalist symbol aimed at keeping a distance from the United States, whose support of India Islamabad resented. It was his successor, Gen. Mohammed Zia ul-Haq, who deposed Bhutto in a coup and later had him executed, who decreed the Islamization of the country. Unlike what happened in the Arab world, where military dictatorships have been a bulwark against Islamic fundamentalism for some decades, Islamization in Pakistan was a weapon used by the army to legitimize its authoritarian rule. Under Zia and the Pakistani military, development of nuclear weapons also helped fuse nationalist pride with Islamic legitimacy.

The support given by Zia, with close cooperation from the United States, to the mujahedeen in Afghanistan fighting Soviet imperialism was crucial for the continued spread of fundamentalism. Countless refugees from across the border were given carte blanche to set up religious madrassas. The dictator encouraged the growth of the Pakistan Muslim League, a political organization, as a way to pre-empt democratic forces, particularly Benazir Bhutto’s Pakistan People’s Party. Nawaz Sharif, who would later become leader of the country, rose to prominence under Zia. After Zia died in an airplane crash, Sharif’s rise was facilitated by the ISI, which was led by Hamid Gul and had by then become the key player in Pakistan’s establishment.

Neither Benazir Bhutto, whose two terms were cut short by the military with help from civilian stooges, nor Sharif, who was manipulated by the military and never able to govern independently, were allowed to establish full civilian authority. Moreover, they failed to see that their common interest, namely protecting civilian institutions from military meddling, was much more important than their legendary rivalry.

In the first decade of the new millennium, Musharraf, who persecuted both Benazir Bhutto and Sharif, and sought to make himself indispensable by becoming an ally of the West in the fight against the Taliban and al-Qaeda in Afghanistan, actually did the opposite of what he promised Washington. Precisely because the secret services on which Musharraf’s power rested had become a bastion of Pakistani Islamization long before his rule, his country’s institutions continued to prop up the very ideology and violent groups that the dictatorship purported to combat. Bhutto’s assassination in Rawalpindi in December 2007, thanks to the negligence of the authorities and the ease with which terrorist fanatics operated in the country under the protection of ISI, was the ultimate proof.

Benazir Bhutto had many flaws. Her second government was marred by corruption scandals, she was never able to consolidate the civilian and secular institutions she championed in her country, and she was slow in grasping the blessings of economic globalization. But she was right about the most important thing: Pakistan’s original sin—the reason for its instability, its dysfunctional politics, and the penetration of its state and society by religious fanaticism—was the brutal influence of military rule in that republic’s short life. And it still is.