After the horrific terrorist attacks of September 11,2001 on New York, Washington D.C. and Pennsylvania which resulted in the unprecedented destruction of the World Trade Center, the Pentagon and the murder of several thousand people from eighty-seven countries, President George W. Bush proclaimed a national emergency and issued an executive order which for the first time in United States history permits the government to hold and prosecute by military commission stateless members of a terrorist organization in an undeclared war. The study examines the nature and purpose of military commissions in American history that provides the context for their role as anticipated by the Bush Administration. It further examines the role of the President as Commander-in-Chief under Article II of the United States Constitution to issue his military orders on military commissions in an age of international terrorism, and the principal substantive procedures issued by the Pentagon to make the commissions fully operational. The study addresses the pivotal role of the United States Supreme Court in deciding landmark national security cases that could well test the very foundation of the balance of power in American government and considers the Administration's authority to declare American citizens as "enemy combatants" and detain them indefinitely without trial; and to hold non-citizen enemy combatants at Guantanamo Bay, Cuba without the opportunity to challenge the basis for their detention in any court of the United States. Finally the study considers whether the war on terror is of such a nature as to warrant expansion of the exercise of war power by the political branches of government. Critical long-term issues that impact on balancing civil liberties with national security interests are identified that must be addressed by the Congress and the Executive in confronting the continuing war on terrorism post-September 11.