In the near future, Earth's oceans have risen and flooded most of its landmasses. This was due to the actions of rogue scientist Zorndyke, who caused the flood that resulted in the death of countless individuals. Many of humanity's remaining cities have been attacked or destroyed by Zorndykes army of half-animal "hybrids". With few options left for survival, the remaining humans wage war against Zorndykes seagoing creations. The submarine forces, including Blue Submarine #6, are humanity's best hope for resolving the conflict. It is revealed that Zorndyke plans to end the conflict in his favor by artificially inducing a polar switch at the South Pole using geothermal energy.