The beginning of the 21st century....

The nuclear weapons disposal facility on Shadow Moses Island in Alaska's Fox Archipelago is attacked and captured by Next Generation Special Forces led by members of FOXHOUND.

The terrorists have got their hands on hundreds of nuclear warheads and they're demanding that the government turn over the remains of Big Boss. They warn that if their demands are not met within 24 hours, they 'll launch a nuclear weapon. Solid Snake is once again called back to duty in a top-secret mission to deal with the greatest terrorist threat the world has ever seen.

His mission is to first single-handedly infiltrate the nuclear weapons disposal site and rescue the two hostages, DARPA chief Donald Anderson and the President of ArmsTech, Kenneth Baker, and then to eliminate the terrorists and prevent a nuclear launch. The time limit is 24 hours. Once again, Snake heads to battle...alone.