Barnett R. Rubin is Director of Studies and Senior Fellow at the Center on International Cooperation of New York University, where he directs the program on the Reconstruction of Afghanistan. ICGA blog
Dr. Rubin wrote an excellent analysis (Pakistan's Power Puzzle - 1st Jan 2008) highlighting that Pakistan Military see themselves as responsible for building a powerful militarized state in Pakistan representing the heritage of Islamic empires in South and Central Asia against the threat from India and the selfish maneuvers of politicians (not necessarily in that order). In the course of doing so, they have enriched themselves and gained control of much of the economy and civilian administration. The military has always aspired to control the judiciary as well, and Musharraf has now restored to that institution the supine illegitimacy that it possessed under General Zia.
The military allies with the U.S. because that is the only way to get the weapons and money for their national security project and to prevent the U.S. from aligning with India.
The goal of the Pakistan military has been neither moderation nor extremism as defined in Washington. Its goal has been to stay in power in order to pursue its national security project, which is also in its institutional interest and the private interest of its members. So why did Musharraf enter into negotiations with Bhutto? As Chief of Army Staff, Musharraf occupied a role similar to that of head of the ruling party in a one-party dominant system. His party, the military, unlike the other parties, is a disciplined cadre organization which, along with its fellow travelers (civilian allies of the military) controls all the key levers of power, including the civil administration and the judiciary. Such control is, it believes, required by the national interest
In order to maintain the essential base of his party's control (U.S. weapons and money) after 9/11, Musharraf had to abandon the military's historic political alliance with the religious right and its allied militants. Read more