The Ship where the announcement from Kenneth Baker,President of ArmsTech,has been attacked by FOXHOUND members. Baker's men are killed by a Cyber Ninja called Gray Fox,who captures him.
Later,Snake is approached by Roy Campbell and Big Boss,who explains the situation. Donald Anderson,chief of DARPA,shows him a Flash Drive that contains a video message from Eli,whose goal is to unleash a powerful weapon. Campbell reveals that his daughter,Meryl Silverburgh is held captive as well.
Snake enters the facility where he locates Baker,who reveals that the weapon is the Metal Gear REX. Schneider appears and kills Baker. Snake is confronted by Gray Fox. He quickly escapes and meet Otacon,who warns him that FOXHOUND has 3 more members: Psycho Mantis,Sniper Wolf,and Vulcan Raven. Snake meets Meryl,who was possessed by Psycho Mantis. He manage to free her and defeats Mantis,breaking his mask. Before dying,Mantis reveals that Eli is Liquid Snake,a clone that wanted to kill Venom Snake until his chance was taken. Snake fought against Gray Fox,who turned out to be a still alive Frank Jaegar.
Meanwhile,Campbell and Boss are held captive by Ocelot and his men. Anderson reveals himself as an imposter,Decoy Octopus. After Vulcan Raven was killed,Snake fought against Sniper Wolf,whom Otacon infatuated with. Liquid Snake wounded her and reveals that he and Snake are both indeed clones of Big Boss. Schneider piloted REX and attacks Snake and Meryl. The two manage to damaged it,injuring Schneider,who was about to kill Snake,but the dying Sniper Wolf fatally shoot Schneider. Liquid Snake escapes as the Self-Destruct system is activated.
With the help of Naomi Hunter,Campbell and Big Boss fought off against the FOXHOUND members. Ocelot and Octopus held them gunpoint. Gray Fox,who was sent there by Liquid Snake,received a change of heart after Snake said about lives at stake and kills Octopus and severed Ocelot's hand before he escapes. Snake,Meryl,and Otacon escapes the facility before it exploded. By the time they return to the base,Snake learned that Ocelot was in contact with someone on the phone while Campbell and Big Boss are held captive.
Mid-Credits:
Liquid Snake meets with Ocelot,who tells him that he'll get answers from the Sons of Liberty.