On June 6, 1991 a chemical weapon called Lucipher-Alpha is released, causing half the Earth's population to perish. This event later became known as "the Catastrophe." Fifty years later in Neo Kobe City, bizarre androids started to appear that kill their victims and assume their identities for unknown reasons. They have the ability to generate life-like human tissue around their robotic endoskeletons. As a result they are indistinguishable from the human victims they imitate. No one knows where they come from or why they do this. They have been dubbed "Snatchers", as a result a special Anti-Snatcher task force known as JUNKER has been assembled.
The player controls Gillian Seed, a member of JUNKER who suffers from amnesia. He is accompanied by a small robot referred to as "Metal Gear", which serves as both a navigator & sidekick for Gillian. Together they aim to put a stop to the Snatcher menace and uncover the mysteries of Gillian's past.