Hayato's city is destroyed by a giant robot, and his parents are killed in the attack. The only friend he has left is his dog Jack, and the only possessions remaining are his mother's shoe and a photo of a man and a woman—who, as his father tells him on his deathbed, are his real parents. Hayato now seeks revenge against the one believed to have sent the robot: the dreaded Ghost Ship, which attacks ships and is rumored to want to wipe out everything. But then Hayato discovers a hidden underground factory belonging to Mr. Kurosio, the man who owns most of the city—and he realizes things are not as Mr. Kurosio has led him to believe. Someone terrible dwells in a castle beneath the sea. Hayato tries to spread the truth to the people, but his life is now at risk from the one who does not want to be exposed. Then Hayato is saved by none other than the captain of the Ghost Ship. Hayato is about to uncover far more than the single secret he has been pursuing.
