Two years after the events of the Shadow Moses Incident, Solid Snake and Otacon, working as Philanthropy, receive intelligence of a new type of Metal Gear being transported through the Hudson River. As Snake boards the tanker, it's seized by a group of Russian mercenaries led by Revolver Ocelot, intent on stealing the new Metal Gear. Fast-forward to the year 2009: the player takes control of Raiden, a rookie agent operating under the order of the Colonel, apparently a member of a reformed Foxhound unit. His initial assignment is to infiltrate the offshore clean-up facility Big Shell and rescue the President of the United States of America, who was kidnapped by members of a terrorist organization known as Sons of Liberty. However, the matters become increasingly complicated as almost everyone Raiden communicates with appears to have things to hide, and it is hard to tell a friend from foe...