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.

As Nagisa, Orine and Yūka travel on the ship headed for the auditions, they meet fellow auditioners Suzuko Kanzaki and Makoto Yokomizo, along with a stowaway named Sonata Shinonome. They soon learn that Chieri Sono, the daughter of a corporate CEO who had introduced them to AKB in their childhood, had apparently run away from home and boarded the ship to the auditions. Whilst searching for her, Nagisa encounters a strange kid who tells her she should turn Chieri in if she wants to survive the auditions. Just then, the ship comes under attack from the anti-entertainment force DES who come to capture the auditioners. Just as the girls are about to be captured, AKB0048 arrive to take on the forces. As Nagisa gets caught whilst retrieving a ribbon her mother gave her, the kid from before rescues her, revealing herself to be none other than Chieri. Chieri gets trapped under a chandelier, but Nagisa refuses to leave her behind.

As all the applicants are gathered, they begin intense idol training which, to their surprise, involves combat skills and self defense. The manager, Tsubasa Katagiri, reveals that, in order to be selected, the applicants must protect AKB during a guerilla concert. As Nagisa and Yūka argue about Chieri's change in attitude, they stumble across AKB0048 practising and learn how hard they practise and how their occasional squabbles help improve each other. The day of the concert come and the applicants find themselves up against the DES, with many of the girls failing under pressure. As Nagisa and Chieri fight together, Chieri gets shot whilst protecting Nagisa. Thankfully, it is revealed the DES attack was simply a simulation using paint balls. Having taken note of their friendship and teamwork, Tsubasa announces that Nagisa, Chieri, Yūka, Orine, Suzuko, Makoto and Sonata have all successfully passed and will become the 77th generation understudies.

As the 77th gen trainees arrive on Akibastar, they are brought to see an AKB concert, which is opened by the two remaining 75th gen trainees, Mimori Kishida and Sonata's older sister Kanata. However, Kanata is not too pleased that Sonata had joined up and ends up arguing with her. Speaking with Mimori, Kanata reveals she joined AKB so she could get revenge on the DES for killing her father and did not want Sonata to face such danger. As dance lessons begin the next day, Kanata becomes frustrated when her instructor criticises her lack of motivation and runs off. However, Mimori reminds her that it is okay to enjoy singing and she soon makes up with Sonata.

As the trainees are given a day off from their lessons, the girls split off into various groups doing various activities with their seniors. Nagisa decides to follow Chieri as she goes shopping, where they meet up with Yūko, who tells them about the last successor of Atsuko Maeda who disappeared during a concert. Meanwhile, Suzuko and Sonata becomes curious about AKB0048's producer, Sensei-Sensei, whilst Yūka and Orine meet with Tomomi Itano and her ancestors. As all of the current members teach the trainees about what gives them inspiration, Nagisa and Chieri decide to follow in Yūko's footsteps.

The trainees are to make their public debut at a handshake event in order to make a strong impression on their fans. As the girls have trouble deciding what to wear for the event, Orine, who wants to succeed Sashiko receives a hateful video mail, threatening to bomb the event if Orine doesn't quit, which leaves her shaken up. After some advice from Minami Takahashi that there will always be haters, Orine decides to attend the event. Despite still being a little shaken, she cheers up when she meets her first fan. Just then, as the kid from the video threat shows up, an explosion goes off, though it turns out to not be because of him, but instead a DES attack. As the others fight off the DES, Orine vows to protect her hater so she can learn how to improve herself, before they are backed up by the Ota, fans who fight alongside AKB in times of need. Afterwards, Orine receives another letter from her hater offering compliment and constructive criticism.

With some of the AKB successors attending a peace ceremony, Kanata, Mimori, Chieri and 76th gen understudy Megumi are chosen to be stand-ins for the next concert. As Chieri's standing in for Yūko invokes jealousy from the 76th gen understudies, they dig up dirt on how her father is a manufacturer of DES weapons. Chieri explains to Nagisa about how she ran away from home when she heard her father's machines were being used by DES. As Kanata chases after Chieri, reminding her that her father should not affect her dream, Minami, Yūko and some other successors who believe Kanata should be made into a successor follow Tsubasa to where she meets Sensei-Sensei. There, they discover a cave full of Kirara, which shows a mirror of who succeeds the original AKB48 member, predicting Kanata will succeed Minami, who does not take it well.

Following the stand-ins concert, Kanata, Mimori and the 77th gen understudies are asked to stand in for a guerilla concert on a planet where the entertainment ban is in full effect, prompting some jealousy from the 76th gen understudies. Meanwhile, Minami is still concerned about what she saw the other day, and acts weird around Kanata. As they make over there, Sae Miyazawa, a former 76th gen understudy, grows concerned about Megumi. As the increased security evokes debate about whether the concert should be cancelled, the ship comes under attack by the DES. Noticing Minami is struggling to stay focused, Yūko and Kanata set off to rescue her as she is overwhelmed by the enemy. As she recovers from her injuries, Minami laments that she does not want to graduate, but she does not want to hold Kanata back either. As Yūko tells Minami that she should focus on her dream above others, Kanata resolves to become stronger.

Due to Minami's injuries, Kanata is asked to fill in for her in an upcoming concert on the snowy planet Thundristar, much to Minami's dismay. As the understudies explore the planet and see how people under the entertainment ban are like, they meet a group of young fans who are looking forward to the concert. As Nagisa sings to cheer them up, Tsubasa decides to hold a multiple co-ordinated concert with the understudies in order to distract the DES whilst the main concert takes place. Before the concert begins, Minami demands to participate despite her injuries, much to Kanata's disappointment. As Kanata escorts Minami after she comes down with a fever at the end of the concert, Minami understands a bit more about Kanata's passion and once again feels she deserves to be Minami more than herself.

Following a meeting with Sensei-Sensei, Tsubasa announces a gravure shoot for all the members, including the understudies. As they arrive on the ocean planet Atamistar, Makoto grows concerned about her appearance, so Suzuko uses a technique to push all the fat up to her breasts. Meanwhile, Yūko confronts Tsubasa, who was a former AKB successor, about the reason why Atsuko disappeared and the center position was abolished, but gets no answers. As Makoto's plan ultimately fails after being stun by a jellyfish, the Kirara glows brightly when Nagisa and Chieri are shot together. As Suzuko explains to Makoto about how she'd rather be an administration member than a successor, Chieri tells Nagisa that she thinks Kirara has chosen her. Meanwhile, Tsubasa meets up with the camerawoman, the former successor of Minami Minegishi and a former Center Nova, who shows Tsubasa the picture of Kirara glowing for Chieri and Nagisa.

Following one of AKB's concerts, it's suddenly announced that the understudies will make their debut performance on Lancastar, Nagisa, Orine,and Yūka's home planet. As the setlist is announced, it is revealed Nagisa will performing a solo song generally sung by those who receive promotions. Meanwhile, Yūka grows concerned when she learns the boy she fell out with back home, Mamoru, doesn't want her to come back. It is soon announced that a new song has been composed by Sensei-Sensei for the understudies, the first since Atsuko's disappearance, irritating Yūko who becomes determined to learn this song herself. As they approach Lancastar, they learn DES have learnt of the concert. As the understudies explore the town and find the school has been abandoned, they encounter Mamoru and his comrade Aoi, who are members of the Entertainment Liberation. They explain what had happened during the past few months, including the arrest of Nagisa's father.

Nagisa, Chieri and Orine manage to evade capture until they are rescued by the WOTA, who offer to help Nagisa rescue her father. Arriving at the detention center, Kanata and Yūka join the WOTA forces in diversionary tactics whilst the rest of the understudies sneak in underground. However, Nagisa's father refuses to be rescued and they are forced to retreat empty handed. Whilst recouping at Yūka's family restaurant, Nagisa hears from Yūka's parents how her father was arrested because he didn't want Nagisa to be forced to quit AKB0048. Due to all the stress she has been feeling, Nagisa ends up losing her voice, so Chieri decides to fill in for her song. Meanwhile, Minami confesses to Yūko that she intends to graduate after the concert, whilst Chieri tells Nagisa not to think about quitting until after their performance.

As Tsubasa recalls some things Atsuko taught her, the understudies, along with the successors, request that they resume the concert. Just then, everyone hears the voice of Atsuko, whose light brings the concert to the detention center. As Chieri offers Nagisa the chance to sing, she gets her voice back upon seeing her family support her and Chieri's Kirara splits in two. The understudies' group performance soon begins, with everyone bathed in a radiant glow as they perform. As Minami fights to protect the understudies from the DES, the Kirara in the holy grounds choose her as Takamina's successor once more, whilst Sensei-Sensei prophesises that one of the understudies will become the next Center Nova. The camerawoman, who was the former successor of Minami Minegishi, predicted that if they glowed brighter, they would disappear. But didn't at the last minute, she falls on her feet, wondering about the Center Nova.

激動の中、ランカスターでのお披露目公演を無事成功させ、以降AKB0048のメンバーとしてファンたちを熱狂させるようになった凪沙、智恵理たち研究生メンバー。そんな中、AKB0048総支配人のツバサから、驚愕の新展開が発表された。それは、先代の13代目前田敦子以来となる『センターノヴァ制度』と、『ニューシングルの選抜総選挙』の復活だった！それぞれの想いに沸き立つゼロゼロのメンバーたちだったが・・・。

TV放送された『AKB裁判』以降、人気急上昇の智恵理。総選挙へ向けて他の研究生メンバーたちもレギュラーのバラエティ番組など新しい企画に取り組むようになり、初めての経験にとまどうメンバーや、新たな魅力を発揮するメンバーたち。一方、襲名メンバーとともにグラビア撮影などに引っ張りだこになり総選挙でも選抜入りを噂される智恵理も、いまの自分の人気に自信が持てずにいた。

新選抜総選挙の途中経過の速報があり、研究生の一人が9位で発表された。異例の研究生選抜入りの可能性に騒然となるファンとメンバーたち。その頃、智恵理は何故か暗い表情で、仕事にも気合が入らない様子。凪沙もまた、自分たちに順位がつけられてしまうことと、それを競い合うことに後ろ向きな気持ちを抱いていた。そんな中、握手会が開催され、その会場で智恵理が見たものは・・・！？

メンバーたちがそれぞれの想いと戦う中、いよいよ新選抜総選挙が開催された。速報にはなかったメンバーの10位入りに沸く観客たち。その声援に応えるべく明るく前向きな決意表明を見せるメンバー。そして次々と順位が発表されてゆくバックステージでは、父親に作られた自分の人気は嘘であると訴える智恵理が、AKB0048を辞める決意をしていた。n

新選抜総選挙の後、選抜入りしたメンバーたちが撮影、収録、取材と多忙の日々を送る中、その差に気落ちする非選抜メンバーたち。しかし、次の強襲ライブが決定し、凪沙たち77期研究生にある重要な任務が与えられる。それは、強制労働のために移送される少年たちの中に紛れ込み、DGTO軍が造った軍事要塞・ベガスターの機密事項に迫ることだった。

研究生の一人が新しい襲名メンバーになることが確定し、襲名披露公演が決定した。アキバスターの地下神殿で襲名の準備を進めてゆく研究生。彼女が誰を襲名するのかの話題でファンやメンバーたちが盛り上がる中、実際に『襲名』を目の当たりにするのが初めてとなる研究生メンバーたちの間には期待と不安が入り混じっていた。そして同じ研究生としてともに頑張ってきたメンバー達も嬉しさとともに取り残される寂しさを抱えていて・・・。

8代目篠田麻里子となった美森に触発され、襲名メンバーも研究生たちも輝きを増していた。「センターノヴァが生まれるときって、他のメンバーもみんなキラキラしてるもんねぇ」。まるでセンターノヴァを肯定するかのようなみぃちゃんの言葉に、ツバサは違和感を覚える。一方、優子はセンターノヴァを目指し、鬼気迫るほどの練習で自分を高めていた。そんな優子にみぃちゃんは、ポジション・ゼロに立つ勇気はあるかと問いかける。

DES軍による秋葉星急襲の知らせは、遠く藍花星にも届いていた。心配する護。時を同じくして、凪沙の父は芸能とはまったく関係のない部署に移動を命じられていた。辞令を出したのはゾディアック本社。はたしてその狙いとは……？一方、智恵理の父の元には、センターノヴァとして目覚めた9代目大島優子の報告が届いていた。それを冷たい表情で聞きながら、彼は娘の可能性に思いをはせるのだった。

みぃちゃんの活躍によって、DES軍の追跡をかろうじてかわしたフライングゲットだったが、システムが大きく破損し、身動きが取れない状態に陥っていた。不時着した惑星で、修復作業に入るツバサ。凪沙たち研究生は周辺の偵察を行うことになった。大切な人たちと引き離され、大切な場所を奪われ、それでも前に進もうとするメンバーたち。そこへ、突然怪しい影が現れて！？

父親と対決することを決意した智恵理は、凪沙と一緒に射手座星へと向かっていた。智恵理の生まれた星、智恵理の育った家……。凪沙が初めて見るその風景は、綺麗だがどこか殺風景だった。智恵理はこの場所で、寂しい少女時代を過ごしたのだという。一方、フランイグゲットでは、ゾディアックの本拠地に乗り込んだ凪沙と智恵理を心配し、WOTAたちと協力して救出作戦を進めようとしていた。

秋葉星奪還作戦の決行が近づいてきていた。練習に励む凪沙たち。だが、智恵理は射手座星での衝撃的な出来事からまだ立ち直れずにいた。このままでは、作戦の強度が下がってしまう！ツバサは焦るが……？一方、秋葉星に潜入していた護たちは、0048の聖地の変わり果てた姿に愕然としていた。D.G.T.O.に占拠され、DES軍が横行する中、なんとか残されたメンバーたちと会うことはできたが……！？

DES軍によるマインドコントロールと工作活動が行われた結果、凪沙たち0048はかつてファンだった人々からも憎まれるようになっていた。むき出しの憎悪をぶつけられ、萎縮してしまうメンバーたち。だが、心が折れそうになりながらも、自分たちを応援してくれた人を信じたい、かつてもらった優しさを信じたいという思いで、全力のパフォーマンスを続けていく。そんな中、新たな襲名キララが……！？