Tanker Chapter
After the Showdow Moses Island incident the Metal Gear's Top Secret Technology was leaked through the black market from Revolver Ocelot(a spy under the command of Solidus Snake which was revealed at the end of Metal Gear Solid). As a result of this Metal Gears appeared all around the globe making Metal Gear more common for nuclear powers. Solid Snake now a member of an Anti-Metal Gear Group called "Philanthropy" discovers that a new form of Metal Gear(called Ray) is in Possesion of the U.S marines and is heading for an unknown destination, now its up to snake to put an end to the new prototype walking-nuke. To stop it snake must infiltrate a tanker on the hudson river which is carrying the Metal Gear Ray. Just as Snake begins his misson the tanker is hijacked by a mysterious armed group called Sons of Liberty......

Plant Chapter
The "Big Shell". an offshore cleapup facility off New York's coast that works as an environmental clean up preservation, Has been overthrown by a terrorist group called "Sons of Liberty", The President who's been on a tour around the facility has been taken hostage. The Sons of Liberty have demanded a huge sum of money for the presidents return. If demands are not met, the terrorist plan to detonate a series of bombs placed around the Big Shell creating an environmental chemical toxin disaster in the area of water and land around. The Governmet has called on Raiden, a rookie of Snakes old allies called FOXHOUND. Raiden must work as snake and infiltrate the facility without the presidents harm and with his presence unseen.......