Takehiko returns from a pre-historic land to his own country which is ruled by the words of the sun god. Only Himiko can hear and understand these messages, and she relays them to the king, his two sons, and an old man named Nashime, One day, Takehiko goes out hunting and becomes lost. While searching for the way back, he meets a beautiful young girl named Adahime, who had followed him out of the pre-historic country. Himiko, who is Takehiko's half-sister, decides she wants him for herself and orders Nashime to bring Takehiko to her. As word gets about that Himiko is having an affair with her half-brother, the king begins to doubt whether she does hear the words of the sun god. Nashime, though, believes the nation cannot effectively exist without Himiko and plans to assassinate the king. As the king attempts to communicate directly with the sun god, the old man stabs him in the back. Meanwhile, Takehiko's affair with Adahime causes Himiko to have him tortured and banished. He returns to the land of aborigines and raises an army to support his armed intervention in the state. But treacheries multiply, and further deaths only bring forth more claimants to the throne.

According to an article by Donald Ritchie in Newsweek, Himiko is set around the 2nd century B.C., when a new culture, Yayoi, was ousting another one, known as Jomon.

Jomon Japan is the land of untouched forests, of barbaric tribes, wandering shamans. Into this world come priestesses from Korea, who establish a new religion, which becomes Shinto. When Himiko falls in love with her half brother, endangering the purity of the new religion, her counsellor has her murdered, so that she may becomes Japan's first divine ruler, the Sun Goddess. To perpetuate the Faith, a young priestess is installed in place of the dead one.

If the story of Himiko is simple, it is rich in nuance. Shinoda states that Japan has never been anything other than a matriarchy, and that the role of the self-demeaning Japanese maiden is one of the most successful of history's camouflages. He also emphasises Japan's enormous cultural debt to Korea.

The closing scenes, in which the past and the present collide, seem to imply that the question of Japan's historic origins has become academic: the tradition of the country is now dead.