Yura Yamato has just arrived at the high school division of Stella Women's Academy, when Sonora Kashima invites her to join a club called "C³". Sonora is the third-year student who became the new head of this club for military survival games. The other members include two second-year students (part-Japanese Karila Hatsuse and G36K-wielding Honoka Mutsu) and two other new students (Rento Kirishima whose family runs a Japanese sweets shop and the really short Yachiyo Hinata).

In the year since the 77th generation understudies joined AKB0048, the Deep Galactic Trade Organization [DGTO] and DES have stepped up their attacks on entertainment. In response, AKB0048 brings back the general elections and the center nova position. The understudies are now thrusted into a new competition directly against the successors. But as AKB0048 brings back policies not seen since Acchan's disappearance, a new more powerful enemy is quietly moving behind the scenes.

Battle Programmer Shirase, also known as BPS, is a free programmer with super hacking abilities who doesn't work for money. What he does work for is certainly something that only people like him would appreciate. But, his demeanor certainly doesn't suit the jobs he is hired for. With the evil King of America causing trouble via the internet, Shirase is nothing but busy as each new adventure brings even more interesting people into the picture.

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!