Chuuta Kokonose is an orphan who lives with his aunt. For as long as he can remember, he's had a voice in his head, but other than that he's a normal boy—right until the day when a strange-looking thing follows him home and teleports him to a place filled with more fantastic creatures. It's a space police station, and Rein Brickke, the Chief of Solar System Department, tells him that he's been chosen by the computer as a possible candidate to join the police force. Misuzu Sonokata, a girl from Chuuta's school with an angelic face and ill temper who turns out to be one of Rein Brickke's subordinates, doesn't think him suitable for such a job. Chuuta, who was shocked at first, decides to take the aptitude test after being urged by the voice in his head and to prove Misuzu wrong.

The 150-year-long stalemate between the two interstellar superpowers, the Galactic Empire and the Free Planets Alliance, comes to an end when a new generation of leaders arises: the idealistic military genius Reinhard von Lohengramm, and the FPA's reserved historian, Yang Wenli. While Reinhard climbs the ranks of the Empire with the aid of his childhood friend, Siegfried Kircheis, he must fight not only the war, but also the remnants of the crumbling Goldenbaum Dynasty in order to free his sister from the Kaiser and unify humanity under one genuine ruler. Meanwhile, on the other side of the galaxy, Yang—a strong supporter of democratic ideals—has to stand firm in his beliefs, despite the struggles of the FPA, and show his pupil, Julian Mintz, that autocracy is not the solution. As ideologies clash amidst the war's many casualties, the two strategic masterminds must ask themselves what the real reason behind their battle is.

Nanba is the world's most formidable prison, built to incarcerate criminals who are too slippery to stay in ordinary confinement. The four inmates who occupy Cell 13 are particularly cunning on that behalf, having escaped every other prison with a perfect success rate. There is Juugo, a specialist in locks who has spent the majority of his life in prison; Uno, a gambler with great intuition; Nico, an otaku whose body reacts strangely to drugs; and Rock, a bruiser with a love for food. The daily shenanigans of the four prisoners always cause trouble for the building supervisor, Hajime Sugoroku, who desperately tries to prevent them from breaking out of Nanba. Nanbaka follows the comedic, sparkle-filled exploits of these prisoners and their guards. From three square meals a day to sports festivals, prison life in Nanba isn't actually that bad—and it is the closest these four have to a home.

The second part of Nanbaka. The prisoners and their guards continue their comfortable lives at Nanba Prison. However, from the shadows emerges a new threat: Enki Gokuu, a person from Samon's past, who has mysterious goals of his own.