In the year 2007 Solid Snake, now a member of NGO Philanthropy, is sent to investigate an U.S. Marine vessal(disguise as an oil tanker) harboring the new Metal Gear Ray. During the investigation Revolver Ocelot appears and steals the Metal Gear Ray, sinking the tanker.
2009, two years later, Raiden is sent on a mission to rescue the U.S. president from the Big Shell facility(build on top of the sinked U.S. Marine vessel two years ago) held hostage by a terrorist group called, Sons of Liberty. Together with the help of U.S. Seal, Lt. Junior Grade Iroquois Pliskin, they will both uncover a conspiracy that began two years ago.