Much has changed since the end of the Great War: the Jovians and Earthlings have allied themselves, Ruri is the new captain of the Nadesico B, and Akito and Yurika have completely disappeared. Boson Jumping has become so popular that a mass transportation network is being constructed utilizing Chulip portals. What lies in these portals, however, is the secret of the Bose particles and the great power they carry. If that secret falls into the wrong hands, it would mean destruction of epic proportions. Now, alerted of a Martian splinter group with dangerous intentions, the crew of the Nadesico is called back to action, to make things safe in the galaxy and maybe even find out what happened to Akito and Yurika.