In Metal Eye, the player takes the role of a young weapons expert named Findhill. His father was apparently involved in a project that dealt with creating artificial life forms. But recently he has disappeared without a trace. Findhill remained alone, in a small town surrounded by vicious monsters. He wants to become a hunter, just like his father once was, to get rid of the monsters roaming the wilderness, and get to the bottom of his father's disappearance and his mysterious project.

The game is a rather traditional Japanese RPG: Findhill and his companions, who join the party as dictated by the course of the story, wander around a vast world map, visiting towns, descending into dungeons, and fighting random enemies in turn-based combat viewed from a first-person perspective. The party can carry different types of weapons, including various guns (rifles, shotguns, etc.) with expendable bullets. Weapons and armor are shared by all the characters and need not be equipped on individual combatants. The player can also purchase robotic fighters (called "Metals" in the game) in shops, who would then join the party and participate in battles, controlled by the AI. There are scenes with nudity and sexual situations in the game.