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.
For a full summary of the Tanker Chapter, see Tanker Incident.
Another two years later and the Big Shell, the offshore clean up facility constructed in its place is taken over by a terrorist faction calling themselves the Sons of Liberty. New FOXHOUND operative Raiden is sent in to neutralize the threat. However, all is not as it seems.