Two years after the events of "Kidô senkan Nadeshiko" (1996), Akito and Yurika are missing and presumed dead, the former foes of the Great War are allies, and the 14-year-old genetically-engineered wunderkind Ruri Hoshino is now captain of the new Battleship Nadesico. When a Martian separatist group initiates a well-planned, well-executed and most of all successful military action, the combined Earth-Jovian government and military are paralyzed by confusion and internal bickering. It is up to Ruri to reassemble the mostly-retired crew of the original Nadesico to take on an unsanctioned mission to bring a halt to the Martian Successors, free their stranglehold on Boson jump transportation, and discover the fate of Akito and Yurika.