The year is 1964, the height of the Cold War. Naked Snake, an agent in the newly formed special forces unit FOX, heads into Soviet territory to help a Russian scientist flee to the West. However, Snake's mentor and mission advisor The Boss, a female soldier known as the mother of the world's special forces, defects to the Soviet Union, taking a miniature nuclear warhead with her. It's prompt use on a Russian research facility brings the world to the brink of war. Now, Snake must return to the USSR on a secret mission to kill his former mentor and avert full-scale nuclear war.