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The United States Department of Defense (DOD or DoD) is the federal department charged with coordinating and supervising all agencies and functions of the government relating directly to national security and the military. The organization and functions of the DOD are set forth in Title 10 of the United States Code.
The DOD is the major tenant of The Pentagon building near Washington, D.C., and has three major components – the Department of the Army, the Department of the Navy, and the Department of the Air Force. Among the many DOD agencies are the Missile Defense Agency, the Defense Advanced Research Projects Agency (DARPA), the Pentagon Force Protection Agency (PFPA), the Defense Intelligence Agency (DIA), the National Geospatial-Intelligence Agency (NGA), and the National Security Agency (NSA). The department also operates several joint service schools, including the National War College.
The Pentagon is known to have had a rivalry with the CIA during the Cold War because they had a fight over budget and over handling military missions and projects (The last bit was especially because of the CIA being responsible for events such as the Bay of Pigs Invasion as well as the Covert ops in North Vietnam, not to mention the funding for Metal Gear RAXA/ICBMG). Lieutenant Cunningham joined the United States Department of Defense when the CIA gave him a desk job after he lost his leg in Vietnam. They also were some of the key people behind the FOX unit rebellion and were hoping to ruin the CIA's reputation as an efficient Intelligence and military agency.
On the Morning of September 11th 2001 at 9.37.am EDT American Airlines Flight 77 crashed into the Western part of the Pentagon after having been hijacked by the Al-Qaeda terrorist group killing 189 people on both the Plane and the building. The Pentagon damage was repaired by September 2002 and a memorial was built for those who were killed.
The DIA were researching Foxdie at the Pentagon during the early 21st century for assassination use. They were also supporting the Metal Gear Rex project in a partnership with ArmsTech Inc. So During February 2005 they sent FOXHOUND and the Next Generation Special Forces to Shadow Moses Island to oversee the test exercise of the new weapon. However, a major setback occurred when both the FOXHOUND unit and the entirety of the Next Generation Special Forces unit had gone renegade, took over Shadow Moses Island, and demanded the remains of Big Boss or else they will launch a nuclear weapon at the United States (However, it's later revealed that the DoD had actually knew that they would rebel that day from having done an investigation on FOXHOUND long before it happened), they sent a rookie soldier, Meryl Silverburgh, to Shadow Moses Island as a standin after some of the soldiers went missing, but it was later revealed that they had done it on the exact same day deliberately in order to blackmail her uncle/birth father, Colonel Roy Campbell.
They were in command of Solid Snake's mission during the Shadow Moses incident in February 2005. The orders for his mission were to rescue DARPA Chief Donald Anderson and Armstech President Kenneth Baker, and to find out if renegade FOXHOUND could launch a nuclear weapon. Later on Jim Houseman Secretary of Defense ordered nuclear strike on Shadow Moses Island. However he was placed under arrest by DIA Colonel Richard Ames for going against the Patriots.