The story begins with a narrative concerning Tokyo in 1908. However, the grave of Taira no Masakado is shown, emphasizing that his curse still persists. Eventually two strange figures appear in Tokyo at the exact same time. One is Yamumasa Hirai, an Onmyoji of the Tsuchimikado Family who has come to give advice to the prime minister as to how to make Tokyo blessed and successful. The other figure is Yasunori Kato, an evil Onmyoji whose wishes to destroy Tokyo completely to appease his ancestors. He employs the angry spirit of Masakado to bring chaos upon the city, by attempting to kidnap a young girl (Yukari Tatsumiya), who is a distant descendant of Masakado. Hirai discovers this and attempts to stop the evil fiend and save Yukari through his own magic. Unfortunately, the two Onmyoji are too equally matched. Thus their battle becomes more of a tug-of-war for Yukari, as well as a test of skills to see which mystic is more proficient in Onmyodo magic. In the end, Hirai takes the fight his temple, where he believes combined power of his own magic and followers should be enough to stop Kato. However, despite the collaboration of all these individuals against the dark Onmyoji, Kato still manages to gain the upper hand by outsmarting Hirai. Kato escapes with Yukari.

Tokyo has been destroyed. Out of the fires of destruction, the citizens of the great city transfer their energy from despair into hope and reconstruction. Eichi Shibusawa's next undertaking is focused on the construction of a massive subway system underneath the city. He employs the talents of Torahiko Terada, a physicist and scientist in the field of Earthquake Studies, to help oversee construction and plot out the project. With the advent of all these undertakings, it appears as though Tokyo will once again breath in fresh life.

But with the reconstruction of Tokyo comes Kato's revival, as the souls of the dead mystics cry out in agony upon seeing their lands being once again desecrated by technology and renovation. Infiltrating the construction sites for the subway tunnel, Kato employs Shikigami and demonic magic to hold the workers at bay while he focuses on a more important task: the awakening of the Underground Dragon. For when Masakado struck down Kato with his power, the black Onmyoji realized that the violent god would never be his ally. Ashamed at his loss, Kato turns to the areas of Feng Shui, where he can work through natural forces that won't consciously oppose him.

After the dragon under the city had been relieved so to speak Kato found another tool for his destruction. The dark Onmyoji employs all his powers to shift the path of the moon so that the force of its gravity will destroy Tokyo.