The movie was meant to be viewed along with 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, filling in on details that leads up to the plot of the movie. However, the game was never translated and released outside Japan.
The Earth and the Jovian Federation have come to an uneasy peace. However, Akito Tenkawa and Yurika Misumaru have both vanished, presumed dead, and a new threat to peace is rising. Ruri Hoshino has now grown up to be the captain of the new battleship, NS-955B Nadesico B, which sets out to solve the mysteries.
Ruri and her two subordinates, Saburota Takasugi and Hari Makibi (who like Ruri is a genetically engineered prodigy and has exceptional control over machines, actually being able to single-handedly control the Nadesico), travel the solar system around to rally the old Nadesico crew. Some of the crew have undergone slight changes. The Aestivalis pilot Ryoko Subaru now sports her natural hair color, but others, such as the pun-loving Izumi Maki, have not changed at all.
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