The game takes place in 1999, when oil stocks are beginning to run out and the world is facing a global fuel crisis. When a brilliant Czech biologist discovers a microorganism that converts crude oil into wholesome fuel, there is hope of resolving the crisis. Dr Kio Marv is, however, abducted under mysterious circumstances, and the responsibility for the whole case is taken over by the Asian regime called Zanzibar Land, which thanks to the discovery of the Czech scientist and access to nuclear weapons wants to gain power over the world. The last hope of humanity turns out to be Solid Snake - a man who alone solved the problem of a similar rank in the first part of the series Metal Gear.