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.

Led by Reinhard von Müsel, the Galactic Empire crushes the Free Planets Alliance in the Fourth Battle of Tiamat. Arriving in the Imperial capital of Odin to a hero's welcome, Reinhard's victory earns him a promotion to High Admiral and the distinguished title of Count von Lohengramm. On the other side, Yang Wen-li safely returns to the Alliance capital of Heinessen without fanfare and reunites with his dear friends. Reinhard and Yang look forward to a long-awaited reprieve. However, at the request of the scheming Duke Otho von Braunschweig, the Imperial High Command orders the new High Admiral to invade the Alliance with a fleet of twenty thousand ships. After the Duke leaks the plan to the Alliance government, three fleets totalling forty thousand ships are sent to counter the incoming attack and recreate the famous Battle of Dagon. But even though Reinhard is outnumbered two to one, he has an ingenious plan—and Yang sees right through it. Will Yang's superiors heed his warning before it is too late?