The conflict begins not on Earth, but in the ancient city of Sodom, where an entity known as God attacks. In this war, the scientists Dante and Medusa, alongside their colleague Satan, fight back using advanced weaponized aircraft. During the battle, divine flames merge the scientists with their machines, transforming them into the first demons. The people of Sodom, freed from being fused into a giant warrior called Adam, are also turned into demons by the same flames. Parts of God then possess other creatures, creating angelic beings. A long war erupts, ending with the demon Dante being defeated and sealed within the Himalayas by the colossal entity Eve, who has Dante's sister Olga embedded in her forehead.

The story then shifts to the modern era. A young man named Ryo Utsugi is plagued by strange nightmares and visions. He is drawn into a conflict between two secret organizations: the Satanists, who wish to revive the demon lord, and the Souls of God, a militant religious army led by his kendo teacher, Sosuke Oshiba, that hunts demons. Ryo is eventually lured to the Himalayas, where the frozen body of Dante is held. In a ritual, he is consumed by the demon lord, but his consciousness survives and takes over Dante's body, leading to a confused rampage through Tokyo.

After this event, Ryo separates himself from Dante's monstrous form, retaining demonic qualities but his own human mind. For five years, he hides as the world is devastated by war between angels and demons. His sister Aya is revealed to be the reincarnation of Olga, Dante's sister, and is forcibly integrated into a newly reformed Eve. Ryo reawakens as Dante, reunites with his old allies like Medusa and Satan, and wages an all-out war against the forces of God. In the final battle, the demons defeat the colossal Adam and Eve. Dante manages to free his sister from Eve, causing God to be defeated and leave the Earth. The narrative concludes the cosmic cycle of rebellion that began in Sodom, with the demons finally achieving victory over their divine creator.