Solid Snake is dispatched at the request of Colonel Roy Campbell to penetrate the terrorists' defenses and neutralize the threat. Snake is also ordered to locate hostages DARPA Chief Donald Anderson, and ArmsTech president Kenneth Baker. Colonel Campbell's niece, Meryl Silverburgh is also held captive in the facility after refusing to take part in the uprising. Snake enters the facility and locates the DARPA Chief in a cell. He informs Snake of the new Metal Gear REX unit housed at the facility, but then suddenly dies of what appears to be a heart attack. Meryl, who is held in adjoining cell, manages to break out and assists Snake in his escape as enemy soldiers are alerted to his presence. Snake then finds the other hostage, Kenneth Baker. Revolver Ocelot challenges Snake to a gunfight, which is interrupted by a mysterious cyborg ninja who cuts off Ocelot's hand. Baker briefs Snake on the Metal Gear project and, like the DARPA Chief, suddenly dies of a "heart attack".
Snake then contacts Meryl via radio, and agrees to meet her in the base's warhead disposal area on the condition that he contacts Metal Gear's designer, Hal "Otacon" Emmerich. Snake locates Otacon in his lab. The ninja reappears, and Snake realizes that it is actually his former ally Gray Fox, whom he believed killed years earlier. Otacon agrees to aid Snake remotely, using special camouflage to procure information and supplies while he remains invisible. Snake meets with Meryl and agrees for her to accompany him on his mission. Meryl gives Snake a PAL key and they head for the underground base. Part way through the base, Sniper Wolf ambushes them, wounds Meryl, and after a brief duel captures Snake.