In the year 2445, a race of hostile aquatic aliens arrives on Earth. One of their ships sits at the bottom of the Pacific Ocean, raising sea levels continuously for 5 years until almost 88% of the surface is submerged. In order to effectively fight the aliens, the fictional Earth Ocean Alliance develops the "Hydras", one-man submarine fighter craft.

The player takes on the role of the last remaining fighter pilot. The objective is to travel through the alien-infested seas and fend off the targets long enough to complete the missions.