As Pakistan braces for a wave of suicide bombings and other confrontations between Islamic militants and government forces following the end of the Lal Masjid ("Red Mosque") siege last month, many people are wondering how the complicated relationship between the government and militants reached such a violent level. While many blame the embattled current President of Pakistan and Chief of Armed Forces Pervez Musharraf for not acting more quickly and decisively against the factors leading to the tensions, his actions alone may not hold all the blame. In fact, the events leading up to and following the Lal Masjid siege can be seen as the culmination of decades of problematic government in Pakistan. The woes of the present have roots in a historically troubled nation and demonstrate the urgent need for institutional restructuring at all levels of government.

One of the most immediate responses to the Lal Masjid siege and the events preceding the confrontation was to ask where Musharraf had been while the Islamic militants had been galvanizing their ranks to the point of becoming a threat. Many, particularly some moderate Pakistani Muslims and US policymakers, question whether or not Musharraf is really trying to rein in militants who seek a Taliban-style government, despite presenting himself as a secularist. Some even believe that Musharraf has allied himself to an extent with the extremists to help maintain his tenuous grip on power. Indeed, the President has been faced with many other crises that have threatened his very political survival. Even before the Lal Masjid siege, many Pakistanis, particularly those who want civilian rule, questioned whether Musharraf should simultaneously be permitted to hold both the office of President and that of Chief of Armed Forces. Many Pakistani lawyers are also angry over what they perceive to be a flagrant abuse of power after Musharraf briefly and unconstitutionally removed Pakistan's Chief Justice from his post following allegations of misconduct (the Supreme Court later ordered him reinstated). For many, it seems that the President has become power-hungry and is trying to stay in command indefinitely.

Pakistanis aren't the only ones who have been trying to pressure Musharraf. The United States recently stated that the Taliban's and al-Qaeda's leadership—including Osama bin Laden—is in Pakistan, even though that country's government continues to claim that the groups are in neighboring Afghanistan. Washington argues that because of a prior truce between Islamabad and the tribes in the Balochistan and North-West Frontier Provinces, Pakistani government forces have not been active in those regions, so tribal leaders there sympathetic to the Taliban are effectively unhindered in pursuing their agendas. As a result, the two terrorist organizations are regrouping. At the same time, Pakistan's longtime ally China has also been trying to pressure Musharraf into taking action after female Chinese citizens were abducted by radicals linked to Lal Masjid who were leading an anti-vice campaign to impose extreme Sharia law on Islamabad. Both the US and China are now wondering why Musharraf failed to act against terrorist elements in his country until they made attempts against his life in 2003 and 2007—he is a moderate Muslim with many modernizing and liberalizing reforms to his credit and is therefore hated by many extremists—or until his government became imperiled, as was the case immediately prior to the siege. Even with his reforms, including giving the press more freedoms than some presses under democratic governments, and even with bringing a degree economic growth to Pakistan, Musharraf appears nevertheless responsible for allowing extremism to take root in his country.

At the same time, however, Musharraf does not deserve all the blame for his country's current problems, the fixing of which may be a job beyond him. Pakistan has had a long history of being a difficult place to run. Much of its land is desert or mountain, meaning that manmade infrastructure is limited. Social organization in such government-neglected areas is largely based around tribal loyalties, and these groups' alliances can suddenly change; as in the case of those that allied themselves with the Taliban and al-Qaeda, such collusion does not always favor of Islamabad. The North-West Frontier Province and Balochistan area is also the homeland of many of the fighters who were at Lal Masjid during the siege, people who present a stark contrast to the moderate and democracy-minded Pakistanis from the more developed cities of Sindh and Punjab. Prior to the creation of Pakistan after the 1947 Partition with India, the troublesome region was an outpost of British rule, and no one was really able to administer effectively the areas beyond the Indus River.

Adding to the balkanization and virtual unmanageability of the country is the fact that past governments, both civilian and military, have had close ties with fundamentalist groups. Musharraf has been the least friendly—even at times outright hostile—to them of all recent rulers. Nawaz Sharif, the man whom Musharraf deposed, had himself flirted with a strain of Islamism related to the Taliban. Pakistan's longest-ruling military dictator, Muhammad Zia-ul-Haq (in office 1978-1988), was personally friends with the leader of Lal Masjid (a man who also fathered two brothers who fought against government soldiers in this year's siege). Inter-Services Intelligence (ISI) top brass were also friendly with the mosque and its organization, and remain sympathetic to the Taliban even when Musharraf has taken action against them. During the 1980s' Afghan-Soviet war, Pakistan openly trained militants for their proxy war against the Soviet adversary. Islamabad later used militants to fight India over the ownership of the Kashmir region, as direct military confrontations bore little fruit: traditional tactics utilizing government forces had led to Pakistan losing its eastern half, which later became Bangladesh. It remains possible that various elements of the government still use militants in the proxy war against India despite Musharraf's open renunciation of such means. So even if Musharraf has been sincere in trying to stop terrorists, the culture of backing the Islamist militants for secular purposes is so deeply ingrained in the Pakistani government's operational culture that even gradual change is difficult.

Although it definitely clear that Islamabad is not a fully reliable ally, blaming Musharraf for his obvious shortcomings does not provide the full picture of how Pakistan developed into a place where militants are free to roam everywhere, help global terrorist networks, and seize mosques. Even the evidence that people can use to show that the President is either helping or fighting terrorists will not explain how they got out of control in the first place. Instead, the recent events surrounding Lal Masjid have revealed the depth of a government culture that has tolerated, aided, and abetted militants' actions for its own purposes, and, incidentally, how hard it is to govern Pakistan. What the country needs is a way to improve control over renegade areas, a renunciation of terrorist groups altogether, and a complete overhaul of its government. Unless these are accomplished, American military action within Pakistan, even if not directed against the government, will become inevitable.