Most of the world's cities have been flooded by the sea. A madman named Zorndyke and his mutant creations threaten the peace and security of the world. A young pilot named Kino sets out to find a man who can aid humanity in their fight against Zorndyke. His name is Hayami Tetsu, a former mini-sub pilot with a past he'd rather forget. But when Hayami and Kino, along with the famous Blue Sub No 6 are thrown into the war by force, the world discovers that Zorndyke may be a madman, but he has reasons for his action that are worth listening to.