CY Girls the game tells a spy-fi story of CG-1 Ice (voiced by Michelle Ruff), the genius hacker and firearms expert on the mission to destroy an information file in the highly secure corporate building in Buenos Aires (where she is navigated by her partner Sancho), and CG-6 Aska (voiced by Mari Iijima), a master female ninja with astonishing athletic ability attempting to avenge the death of her father in a secret village in Japan (where she is navigated by her brother Kogetsu).

Metal Gear Solid follows Solid Snake, a soldier who infiltrates a nuclear weapons facility to neutralize the terrorist threat from FOXHOUND, a renegade special forces unit. Snake must liberate two hostages, the head of DARPA and the president of a major arms manufacturer, confront the terrorists, and stop them from launching a nuclear strike. Cinematic cutscenes were rendered using the in-game engine and graphics, and voice acting was used throughout the entire game.

On June 6, 1996 (1991 in the Japanese versions), a biological weapon known as Lucifer-Alpha under development in Chernoton, Russia, is released into the atmosphere, resulting in the death of 80% of the Eurasian population which in turn results in the death of half of the world's population. The contaminated area becomes uninhabitable for a decade, when Lucifer-Alpha mutates into a non-lethal form. This tragic event later becomes known as "the Catastrophe". Fifty years later, in 2047 (2042 in the Japanese versions), a breed of artificial life-forms or bioroids known as "snatchers" began appearing in the artificial island of Neo Kobe City, killing their victims and taking their place in society. Nobody knows exactly what they are or where they come from. As Gillian Seed, an amnesiac working for an Anti-Snatcher task force called J.U.N.K.E.R., the player's goal is to track down the source of the snatchers and discover Gillian's mysterious connections with them. The story takes place in three acts.