The Onmyou Taisenki manga does not tell the same history as the anime. The story happens years before the events in the anime.

The main character, Yakumo (who also appears on the anime, as a teenager) is the son of Monju, the chef priest of the Taihaku Temple, in Kyoto. Yakumo also trains the In, with a baseball ball. In this temple, a Toujinshi (闘神土, literally 'god of war'), and Monju's former teacher, Mahoroba, is imprisioned.

The problems start when Mahoroba escapes, gains power, and transforms Monju into stone. Yakumo is called by a Zero Drive, which was one of the treasures of the temple. This Zero Drive handles Byakko no Kogenta. The story of the manga is about Yakumo's first steps with a Shikigami, training with Idzuna (Taihaku Temple's shrine maiden) and seeking Mahoroba through various Japanese historical dates. Famous Japanese historical characters such as Oda Nobunaga can be seen on the manga.

From Abyssal Chronicles:
For a long time now, the Capital Kingdom of Regunum has kept its dominance over the land during the raging wars, and kept the world at peace. There are, however, the recent appearances of humans who held within them great mystical power, the "inousha" (literally translated as "a person with a gift/talent"). The people started fearing these inoushas, and began to detest them. Because of this, the capital of Regunum carry out a movement to seize and capture all inoushas within the land to keep the people at bay. At this time, Ruca, the son of a merchant living in Renugum, discovers that he also holds the same mystical power.