When an extraterrestrial organism called "Savage" attacks humanity, the only technology capable of fighting the enemy is a weapon known as "Hundred." Hayato Kisaragi, a survivor of a Savage attack, is a teenager who boasts the highest compatibility level with this technology and, as a result, is invited to hone his skills at Little Garden, a prestigious military academy located on a battleship. During his intense training for the upcoming battle, he immediately attracts the attention of several female classmates and becomes involved in various incidents as he attempts to fight the creatures that now inhabit Earth and threaten its safety.