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 who wields this Hundred, Kisaragi Hayato enrolls in the marine academy city ship Little Garden. However, Hayato feels a strange yet familiar sense of incongruity towards Emile Crossford, his roommate who somehow knows him from somewhere. On top of that, as soon as he enters the school, he is challenged to a duel by the Queen, the school's most powerful Slayer, Claire Harvey.