Set in the 18th century, the show follows the Shogun Yoshimune, who likes to disguise himself as a low-ranking samurai and go into his capital of Edo to see the life of the common man, as well as to seek out and punish evildoers who would hurt his citizens. He is aided by Magistrate Oo'oka and a vivacious fireman, Tatsugoro, as well as a rotating cast of other recurring characters.

Along with Zenigata Heiji and Mito Kōmon, it ranks among the longest-running series in the jidaigeki genre. Like so many other jidaigeki, it falls in the category of kanzen-chōaku, loosely, "rewarding good and punishing evil."

In an alternative feudal Japan, a strange disease that only affects males caused a massive population reduction, leaving females to fill the vacant jobs, therefore changing the social structure. Now, 80 years after the initial outbreak with a 1:4 male:female ratio, Japan is a completely matriarchal society. Females hold all important political positions, and males are their consorts. Only the most powerful female—head of Tokugawa shogunate—may keep a harem of handsome and unproductive males, known as "Ōoku".

Commanding shoguns and samurai warriors, exotic geisha and exquisite artisans—all were part of the Japanese “renaissance”; a period between the 16th and 19th Centuries when Japan went from chaos and violence to a land of ritual refinement and peace. But stability came at a price: for nearly 250 years, Japan was a land closed to the Western world, ruled by the Shogun under his absolute power and control. Japan: Memoirs of a Secret Empire brings to life the unknown story of a mysterious empire, its relationship with the West, and the forging of a nation that would emerge as one of the most important countries in the world.