Humanity is plagued with attacks by a race of sea mutants dedicated to eradicating mankind. Our last hope is the Blue Submarine No. 6 and her crew, made up of the best personnel available as they fight for the fate of all mankind.

After surviving another undersea battle with Zorndyke's forces, the crew of Blue Submarine No. 6 returns to base for repairs. While on base, Tetsu continues to display his trademark lack of concern for authority and continues to annoy Mayumi.

Tetsu drifts in the open sea. As his life flashes before him, he begins to black out. But when he comes to, he finds himself resting on the hull of a half-sunken ship. His savior is one of the enemies.

The poles are shifting and most of the Earth's land is now underwater! The scientist Zorndyke has created a race of beast people to challenge the humans for global supremacy. But who is the real enemy - Zorndyke or humanity itself?