The story begins with a man known as Snake, a young woman named Consuela Alvarez, and two pilots named Dave Copeland and Roddy Louiz, flying into the United States illegally when they are arrested by the FBI. After being caught, Snake is pressed into a mission by his captor, an FBI agent named Dalton. Snake agrees to the job to free his friends and clear his name with Dalton. Snake's initial objective is to infiltrate a research facility operated by SaintLogic (called "StrateLogic" in the Japanese version), a military arms manufacturer, located on an isolated North American island. Dalton is investigating SaintLogic for inhuman actions towards children, and utilizes Snake's abilities to infiltrate SaintLogic and uncover the truth behind their business practices.