In the year since the 77th generation trainees 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 announces 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 are later freed by the rest of AKB0048 with the help of WOTA. The trial itself made Chieri famous throughout the galaxy and receives more work (such as photoshoots). Cheri's father starts developing artificial Kiraras while Tsubasa becomes curious as to how were able to break into Kasumigastar so easily earlier. The understudies are now thrown into a new competition directly against the successors especially when the general election is approaching.
Soon later, the results of the general elections are announced with Hikari (Yuuko) 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 discover a hidden illegal casino there. The girls target the nuclear reactor hidden in the base, shut down the casino and escape with Higashino, the DES guard who 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 and 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 orders 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 hold 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 meet with the creatures there. A new bond of friendship is 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 of one of Zodiac's ships, taking them to Sagittariusstar so that Chieri can confront her father face to face. Chieri finally reaches her father and is told to exhibit her singing skills but witnesses her father assassinated by a person unknown in front of her when it just seems as if he became friendlier towards his daughter again. Nevertheless, Chieri and her teammates show their fighting spirit to reclaim Akibastar. Back in Akibastar, the people there shows sign of hatred towards AKB because they feel betrayed by their retreat and turned against them since the DES is strongly controlling the planet. Despite this, 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 to withdraw, returning peace to Akibastar with Nagisa promoted as Atsuko Maeda the 14th and Chieri as the new Center Nova.