The story begins in the near future, when the Earth's oceans have risen and flooded most of the sea-lying land on Earth. The rogue scientist Zorndyke caused the flooding, which killed countless individuals, and most of humanity's remaining cities have been attacked or destroyed by Zorndyke's army of half-animal "hybrids". The remaining humans begin to wage war against Zorndyke's seagoing creations for simple survival. Humanity's best hope for a resolution to the conflict lies with its submarine forces, among which is the focus of the story, Blue Submarine #6. It is revealed that Zorndyke is attempting to decisively end the conflict in the favor of his hybrid children by artificially inducing a polar switch using geothermal energy at the South Pole.