When an extraterrestrial organism known as "Savage" attacks humanity, the only technology capable of fighting the enemy is a weapon called “Hundred.” Hayato Kisaragi, a survivor of a Savage attack, is a teenager with the highest compatibility level for this technology and is consequently invited to hone his skills at Little Garden, a prestigious military academy located on a battleship. During his intense training for the battles to come, he quickly draws the attention of several female classmates and becomes involved in various incidents as he fights the creatures now inhabiting Earth and threatening its safety.