Deep-sea archeologist Hiroshi Ibuki is the member of the digging team working at the bottom of the sea hoping to uncover the origins of Earth's existence but instead uncovers a mysterious colony of bacteria which gives off light similar to the Aurora Borealis. The ancient bacteria, once revived, attempt to make the world habitable for themselves - a process that would bring Earth back to its early primal form, killing all current life in the process.
Less than a year after Geist activated the Death Force, which decimated most of Jerra's population, he has kept himself busy by dismantling the Death Force machines one by one. Most of the remaining human population have fled to a remote haven run by a warlord named Krauser. Krauser is another MDS unit, MD-01, who has a technology that hides his mobile fortress from the Death Force.