9/11 Commission Recommendations Implementation Act of 2004 - Establishes a National Intelligence Director to manage the National Intelligence Program.
Empowers the Secretary of Defense with lead responsibility for directing and executing paramilitary operations, whether clandestine or covert.
Establishes a National Counterterrorism Center for strategic analysis concerning transnational terrorist organizations with global reach.
Requires the President to direct the head of each appropriate Federal department or agency to identify and prioritize actual or potential terrorist sanctuaries throughout the world. Requires a national strategy to destabilize identified sanctuaries. Authorizes the President to support the Government of: (1) Pakistan in its efforts against extremists; and (2) Afghanistan to extend its authority over such country.
Directs the Secretary of State to establish programs to promote greater familiarity with American society and values among the general public and select audiences in Muslim countries.
Directs the President to: (1) strengthen counterproliferation efforts against weapons of mass destruction; and (2) track the financing of terrorist organizations and prevent money laundering for their benefit.
Requires the Secretary of Homeland Security to: (1) integrate U.S. border screening systems with Federal security sites within the U.S. transportation system and sites containing vital national facilities; (2) complete a biometric entry and exit screening system for persons entering and departing the United States; (3) develop a plan for the allocation of limited transportation security resources; and (4) improve aviation screening.
Requires: (1) the sharing of information for purposes of protecting the national security; (2) the establishment of a board to oversee Federal adherence to civil liberties; (3) that all U.S. emergency response agencies adopt the Incident Command System and unified command procedures; (4) the promotion of private sector emergency preparedness; (5) both Houses of Congress to pass separate intelligence appropriations bills; (6) a specialized and integrated national security workforce at the Federal Bureau of Investigation; and (7) regular adequacy assessments of the strategies and planning of the United States Northern Command to defend the United States against military threats.