Three years after the war between Jupiter and Earth, we follow Ruri Hoshino as captain of the Nadesico-B space cruiser. Peace seems secure, and a new colony project called the Hisago Plan is well underway -- until it is attacked by a rogue, unknown Aestevalis that has a exceedingly skilled pilot controlling it. Who is this renegade pilot, and could his arrival have anything to do with the disappearance of Akito and Yurika many years ago? Ruri will have to delve deep into her own past and that of her former crewmates as a new far-reached conspiracy unfolds...
Half a year has passed since Sagara Sousuke took up the job of protecting Kaname Chidori and has started living like a normal teenager for the first time. A former child soldier, his view on the perils of everyday life is highly unconventional and in frequent need of violent adjustment; Chidori can only hope her endless assault will eventually get him used to normal life. But a shadow looms over their happy days as Sousuke's employer, the private army called Mithril, is attacked by a new unknown enemy. Suddenly outgunned, can Mithril afford to keep one of their best playing around?