The story is a direct sequel to Nadesico: The Blank of Three Years, a video game for the Sega Saturn that takes place immediately after the TV series ends, and before the movie begins.

Meanwhile, a new threat to peace is rising in the form of the "Martian Successors" (A splinter group of the original Jovian Federation who wish to continue the war and take revenge on the Earth and Nergal and bring about a new world order).

A 15-year-old Ruri Hoshino is now the new captain of the highly mobile battleship Nadesico B and has earned the respect and awe of many in the Military thanks to her unparalleled skill with machines, made her gains the nickname "Cyber Fairy".

Akito had been tortured, his brain severely affected to the point of not being able to taste anything (thus being unable to cook) and his skin shining white like a comic book.

Nadesico: The Blank of Three Years, a video game for the Sega Saturn, was released September 23, 1998, one month after Prince of Darkness hit theaters.