Bowser's airship fleet wreaks havoc on the Mushroom Kingdom. The King is missing, presumed dead. The princess is on the run. A couple of plumbers answer the call of duty and sign up to fight. Now Mario, Luigi, and a team of old-school video game characters are thrown into the gritty new world of first-person shooters.

Video game villain Bobby Kotichovich is creating a new weapon - Modern Gear! Snake and Ghost set aside their differences to defeat Kotichovich and save the world.