The story begins with the Hundred, the only weapon that can counter the mysterious Savage life form attacking Earth. To become a Slayer (master of military arts) who wields this Hundred, the main character Hayato Kisaragi successfully enrolls in the marine academy city ship Little Garden. However …
"I wanted to meet you, Hayato!!"
"W–who are you…?"
Hayato feels a strange yet familiar sense of incongruity towards Emil 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!