When an extraterrestrial organism known as "Savage" attacks mankind, the only technology capable of combating the enemy is a weapon known as “Hundred.” A survivor of a Savage attack, Hayato Kisaragi is a teenager boasting the highest compatibility level with the aforementioned technology and as a result, is invited to master his skills at Little Garden, a prestigious military academy aboard a battleship. During his hard preparation for the struggle ahead, he instantly draws the attention of several female peers and becomes involved in a variety of mishaps as he strives to fight the monsters who now occupy Earth and endanger its safety.