After an interplanetary war at the beginning of the 21st century, planet Earth has been left in ruins, with much of its ecosystem completely destroyed. Because it was no longer possible to live a normal life on this planet, the inhabitants are forced to move on to other planets where life will, hopefully, be more comfortable. The Deep Galactic Trade Organization, a totalitarian government that affects many of the newly inhabited planets, has somehow come to the conclusion that music is a source of evil, and that it must be banned and destroyed for good. The talent group AKB0048 is soon formed, based on the original AKB48 members that once lived on Earth. Even though their music is now considered universally illegal, they make it their mission to bring their music back to life by travelling from one planet to another and holding as many concerts as they possibly can. They must undergo a whole new set of training methods in order to become the best that they can possibly be, while also avoiding the constant danger of being arrested because of their music. Join interplanetary popstars AKB0048 as they try to save the world－with music!

On the beautiful banks of the Arakawa River, it is lively as ever. Now known as "Recruit," Kou Ichinomiya has adjusted to the troubles his unconventional neighbors brew daily. However, the atypical scene is about to get even rowdier when their community adds a couple of oddball enthusiasts: a tall, muscular woman calling herself Amazoness, followed by her loyal Tengu henchmen; and Captain, self-proclaimed Commander of Earth's Defense Force against Venusians. In spite of all the commotion, Recruit gradually learns more about his lover Nino and the story that shaped her.

Takao Kasuga, a high school student fascinated by poetry, reveres Charles Baudelaire and even decorates his room with the poet's portrait. On a normal day, Takao forgets his copy of The Flowers of Evil in the classroom. When returning to retrieve it, he steals the sports garments of Nanako Saeki—a model student who Takao calls his muse and a femme fatale. Deeply ashamed of his act which he sees as a sin and what others see as a crime, Takao realizes with horror that Sawa Nakamura, his classmate and social outcast, knows about his theft. Blackmailed by her, Takao is now forced to partake in Sawa's disturbing fantasies, lest she reveals his deeds to everyone. Caught in a negative spiral of increasingly traumatic experiences, will Takao be able to break free from Sawa's thorns and atone for his sins?

Kaori Sasaki—a member of Uchihama Academy's Astronomy Club—confesses to Sou Akiyama, but later that evening, she dies in a tragic road accident. Her friends and fellow club members mourn her death in a local hospital. Yet she shows up to school the following day, and no one senses anything amiss. The day finishes without any unusual incidents, and the group of friends plans for the upcoming cultural festival. Suddenly, the room is shaken by an unnatural earthquake. Everyone splits up to investigate—except for Nagisa Hanamiya, who stays behind. As everyone leaves, Nagisa notices that the odd relic-like cube that she was toying with starts emitting a strange blue light. Meanwhile, Sou stumbles upon an unconscious, naked girl lying in a pool of water. Ushinawareta Mirai wo Motomete follows the Astronomy Club's increasingly bizarre adventures—from dealing with ghosts to quelling unrests between student clubs. All the while, they unravel the circumstances behind the sudden appearance of a new transfer student.