A mysterious life form known as Savage is attacking the Earth, and there is only one weapon that can counter it: the Hundred. To become a Slayer, a master of military arts able to wield a Hundred, Kisaragi Hayato enrols in the marine academy city ship Little Garden. However, Hayato feels a strange yet familiar sense of incongruity towards Emile Crossford, his room-mate who somehow knows him from somewhere.