Four years after former FoxHound hero Solid Snake saved the day on Shadow Moses Island, a new terrorist organization known as Dead Cell has hijacked the environmental cleanup facility known as the Big Shell and taken the President of the United States hostage. In response to their threat, FoxHound agent Raiden must join forces with a mysterious Navy Seal known as Pliskin to rescue the President and neutralize Dead Cell, whose leader is said to be none other than Solid Snake himself!