The Nuclear Weapons disposal facility on Shadow Moses Island in Alaska's Fox Archipelago was attacked and taken over by Next Generation Special Forces, being lead by members of Fox Hound.
They're currently demanding that the government of the United States turn over the remains of Big Boss and they say if their demand is not met within 24 hours, they'll launch a nuclear weapon.
Solid Snake (you) has two mission objectives. The first is to rescue the DARPA's chief, Donald Anderson, and the President of Armstech, Kenneth Baker. Both are being held as hostages. Secondly, Snake has to investigate whether or not the terrorists have the ability to make a nuclear strike, and stop them if they do.