The movie starts off after the events of Episode 3, when Kisaragi had sunk. The Mikawa Fleet (Furutaka, Aoba, Kako, Kinugasa and Tenryuu) are in the middle of Night Battle. Choukai uses Searchlight and gets medium damage, but they win in the end. A New Fleet Girl gets "dropped", emerging from the sea. It is Kisaragi. Kisaragi is brought back to the temporary base in Solomon Islands, but she is suffering from PTSD and has amnesia, unable to remember anyone from back in the anime, excluding Mutsuki...
When Utopia More discovers an ancient record that holds the key to unlocking the secrets of the universe, she becomes the target of the ruthless Gypsy Doc of the Pirate Guild. Utopia finds herself saved by the easy-going yet legendary space pirate, Cobra, whose custom made Psychogun makes him a force to be reckoned with. Together, the two of them attempt to stop Gypsy Doc (along with Cobra's revived arch-nemesis, Crystal Boy) and his efforts to steal the record and use its secrets to rule the universe.
