Mankind is under attack from an extraterrestrial entity named "Savage." The sole weapon capable of combating this foe is the "Hundred." Hayato Kisaragi, who survived a previous Savage attack, is a teen with the highest compatibility level with the technology needed to fight them. Because of this, he's invited to attend Little Garden, a prestigious military academy located on a battleship, to hone his skills.
During the intense training to prepare for the upcoming battles, Hayato catches the attention of several female students and is pulled into various incidents as he fights back against the creatures that now reside on Earth, endangering its security.