At the start of the 21st century, an interplanetary war broke out. Earth’s ecosystem was severely damaged, and humanity was forced to flee the planet, hence begin a new history with the Star Calendar starts from the year 0000. In several planets of this new society led by a totalitarian government, the Deep Galactic Trade Organization [DGTO], things that “disturb the heart” like music and art are forbidden. The legendary idol group AKB48 is later resurrected as the interplanetary troupe AKB0048, made up of girls who carry on the title and spirit of the original members. With the government see the existence of the idol group as illegal, the idol group could not held their concert officially. AKB0048 also changed their concept from “idols you can meet” to “idols who see fans”. Held as heroines by some and labeled as terrorists by others, they take up arms to bring their music to their fans wherever they are. The story follows a group of young hopefuls as they train to become the next generation of AKB0048.
In the year since the 77th generation trainees (kenkyūsei?, 研究生, also understudies) joined AKB0048, the Deep Galactic Trade Organization [DGTO], a totalitarian galactic government and its national armed force, Destroy Entertainment Soldiers [DES] have stepped up their attacks on entertainment. AKB0048 continue their next stage and performs the concert at Atamistar. Manager Tsubasa announced to bring back the general elections and the Center Nova position. The same night after the concert, Chieri, Ayako and Sonata were caught by the DES to be tried in a High Court in Kasumigastar, the DGTO’s capital, but was later freed by the rest of AKB0048 with the help of WOTA. The trial itself made Chieri famous throughout the galaxy and has been getting more work. Cheri’s father started developing artificial Kiraras with Tsubasa becomes curious as to how were able to break into Kasumigastar so easily earlier. The understudies are now thrust into a new competition directly against the successors especially when the general elections is approaching.
Soon later, the results of the general elections was announced with Hikari (Yuko) announced winner of the top 10 list along with other successors in their respective rankings. Also included in the top 10 list were 77th generation trainee Chieri Sono in 6th place and 75th generation trainee Mimori Kishida in 10th place. The elected members are chosen for a concert on Baltistar, a planet completely under the entertainment ban. Meanwhile, the 77th generation of trainees are chosen to infiltrate a nearby military base undercover in order to investigate reports of people visiting the base and discovered a hidden illegal casino there. The girls targeted the nuclear reactor hidden in the base and shut down the casino and escape with Higashino, the DES guard helped them in the process. Some time later, the Kirara of Succession show the original Atsuko’s image, foretelling that someone may succeed her soon. Mikako is brought in as the group’s official camerawoman as the group rehearse for a concert. After the rehearsal, Mimori comes down with a succession fever, Nagisa is chosen to stand in for her in the concert.
Mimori recovers from her fever and debut as a successor, inherited the name of Mariko Shinoda the 8th. Mikako unknowingly informs Chieri’s father of the three conditions required for initiating the Center Nova phenomenon. Knowing this, the latter order his company Zodiac, under the DES to go after an element known as Dualium that is hidden in Akibastar by launching a DES Force attack there one day when AKB held another concert, putting the city into chaos and forcing AKB to struggle against the DES. AKB retreat from Akibastar due to escalating battle. During DGTO’s occupation of Akibastar, AKB0048 barely manage to escape the DES in their ship and arrive above a strange planet to be repaired because it sustained the DES attack. The trainees are sent to gather data on the planet they landed on and in the process met with the creatures there with a sign of new friendship was made as they defend the planet together and defeat the Zodiac machines that came out of the blue to attack the planet for dualium but sacrificing the nature there. Chieri and Nagisa later sneak on board Zodiac’s a ship taking them to Sagittariusstar so that Chieri can confront her father face to face. Chieri finally reached her father and was told to exhibit her singing skills but witnessed her father assassinated by a person unknown in front of her. Nevertheless, Chieri and her teammates show their fighting spirit to reclaim back Akibastar. Back in Akibastar, the people there shows sign of hatred towards AKB because of feeling betrayed by their retreat and turned against them and the DES is strongly controlling the planet. Despite these, Chieri, Nagisa and the others combine their feelings with the nameless emotions across the galaxy and fight back with love and music, getting the DES withdraw, returning peace to Akibastar with Nagisa promoted as Atsuko Maeda the 14th and Chieri as the new Center Nova.