At the height of the Cold War, America's finest operative — the legendary soldier known as The Boss — defects to the Soviet Union. In that same moment, an extremist named Colonel Volgin launches an American-made portable nuclear missile at the Soviet design bureau OKB-754, igniting an international crisis. To clear its name and stave off World War III, the United States sends a man called John — codenamed Naked Snake — deep behind enemy lines, with orders to assassinate the very woman who once taught him everything he knows.