In 1990 (previously 1986), in Elysion; the five Bronze Saints Seiya, Hyōga, Shun, Shiryū and Ikki, having wreaked havoc in the Underworld's army and succeeding in resurrecting the God Cloths, engage the god Hades in a final duel to the death.

During the battle, Hades remembers that he has seen Seiya's face before and comes to the conclusion that he faced him before. He thus starts reminiscing about his previous host body, and the story starts 247 years prior, in the 18th century.

The protagonist, the Pegasus Saint of this era, is an orphan who is best friends with a boy named Alone, the host of Hades. Former Bronze Saints Dohko and Sion, two prominent characters in Kurumada's original manga as the sole survivors of the holy war of that century, have just been promoted to Gold Saints and eventually the two duos meet.