On Oct. 9, 2004, Deputy Secretary of Defense Paul Wolfowitz approved Department of Defense Directive 5134.9, which was 19 pages that chartered the mission and function of the recently created Missile Defense Agency.

This document replaced the June 1994 version of the directive that had chartered MDA's predecessor the Ballistic Missile Defense Organization.

This directive for MDA reflected the new circumstances in which the world operated. The War on Terror had replaced the Cold War. As President George W. Bush observed in National Security Presidential Directive 23 in December 2002, "The contemporary and emerging missile threat from hostile states is fundamentally different from that of the Cold War and requires a different approach to deterrence and new tools for defense."

As a result, the mission of the organization shifted from "enable deployment," "develop options," and "demonstrate advanced technologies" to "MDA shall manage, direct, and execute the development of the Ballistic Missile Defense System" … to achieve specific DoD priorities.

These were:
* To defend the United States, deployed forces, allies, and friends from ballistic missile attacks of all ranges in all phases flight.
* To develop and deploy, as directed, a layered BMDS.
* To enable the fielding of elements for the BMDS as soon as practicable.
* To provide capability in blocks, improving the effectiveness of fielded capabilities by inserting new technologies as they become available.

In other words, MDA would conduct the necessary research and development and test and evaluation to deploy a consolidated BMDS that would address the threat posed to the nation and deployed forces in the boost, midcourse and terminal phases. To ensure that the system was state-of-the-art, improvements -- emerging technologies - would be introduced as they matured through a series of blocks (biennial increments), in a system of spiral development. Again erasing the distinction between national and theater missile defense, the BMDS elements included the Aegis Ballistic Missile Defense; Terminal High Altitude Area Defense; Airborne Laser, Command and Control, Battle Management and Communications; Ground-Based Midcourse Defense; Kinetic Energy Interceptor; Patriot Advanced Capability-3; BMDS Sensors and the Space Tracking and Surveillance System.

In a change from previous charters, the MDA director was designated the BMDS acquisition executive for all programs funded by MDA in accordance with the streamlined Defense Acquisition System. The director also received milestone decision authority for these programs, up to Milestone C. Production and Deployment decisions rested with the Under Secretary of Defense for Acquisition, Technology and Logistics, with the approval of the Senior Executive Council. The charter also tasked the under secretary to advise the Secretary of Defense when missile defense assets, still in research and development, were available for emergency or contingency use.

Finally with the formal withdrawal from the Anti-Ballistic Missile Treaty in 2002, foreign participation in missile defense was no longer restricted. Recognizing this fact, this new MDA charter recognized the potential for foreign participation in the BMDS program, over and above technical cooperation programs, and authorized the Director to negotiate and conclude international agreements.

This document remained in effect until September 2009, when a new directive revised the review structure.