In a dystopian future where music is deemed illegal, AKB0048, successors to the idol group AKB48, rebel against the government to bring music to people's hearts. In the year 0048, three thirteen year old girls, Nagisa Motomiya, Orine Aida and Yuuka Ichijō, decide to audition to become members of AKB, although Nagisa has trouble singing due to the restrictions placed upon her by her father. As the girls hear they've passed the first round of auditions, Nagisa becomes downhearted as she wouldn't be allowed to go. However, after hearing about Yuuka's and Orine's reasons for wanting to join AKB, Nagisa decides to join Yuuka and Orine and head off to the auditions.
辺境の星で暮らす凪沙、智恵理、優歌、織音は幼き頃、禁断のゲリラライブに衝撃を受ける。
そして、星暦0048年憧れの「AKB0048」オ―ディション開催を知る。
現実と夢の狭間で葛藤する少女達が選ぶ道は・・・