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Marika is living the normal life of an average girl in space: attending her school's yacht club, keeping up with the latest trends, and working part time. One day can change a lot, however. Not only was her late father a notorious space pirate, he was also the Captain of the equally notorious Benten Maru! What's worse, she's just inherited his position and the pirate's life that comes with it.
In order to become a stronger person, a young boy named Hiroshi stows away on a freighter bound for planet Daibaran. The freighter comes under fire from an Afressian fleet, but is saved by the appearance of a mysterious spaceship. Upon reaching his destination, Hiroshi finds a job in one of the roughest saloons on the planet in order to toughen up, but ends up in an unfair fight when the Afressians begin to search for the one who attacked them. He is eventually rescued by a cloaked woman, who reveals herself to be Emeraldas, captain of the mysterious ship that saved him before. Stung by two defeats, the Afressian leader Bararuda decides that there is only room for one queen in space... but can a single ship piloted by one woman stand against the fury of a whole empire?
When Tadashi Daiba's father is murdered by invaders known as the Mazon, he becomes frustrated in the face of the Earth government's flippant attitude. Landing himself in prison, Tadashi finds himself invited aboard the battleship Arcadia, controlled by none other than the legendary Captain Herlock. Joining his crew on their journey through space, Tadashi's future will lead him to confront not only the Mazon, but the many other forces across the universe threatening humanity's very existence.