In the near future, the oceans have risen, causing all land at sea level to be flooded. With the expansion of the oceans, humanity has found a new enemy in Zorndyke. A war has erupted between the surface dwellers and the sea dwellers, and mankind is placing all of its hopes in the new vessel Blue Submarine No.6 and her crew.

Mayumi Kino is a young, devoted pilot. Her most recent mission is to get Tetsu Hayami to rejoin the Blue Fleet. However, he refuses and angers her, so she leaves. Later, however, the two meet again under more dire circumstances and they start to work together. Even in the thick of battle, however, it becomes clear that they don't see eye to eye...