A Holy War, from ancient mythology, where the Goddess Athena and Hades have fought against each other while defending the earth repeatedly over the span of 200 years. The story takes place in 18th century Europe, 243 years prior to the original "Saint Seiya" Three small children, Tenma, Alone, and Sasha have all shared a very happy childhood together. Tenma who is quite aggressive but upstanding has moved to Sanctuary to become a saint. It is there that he is reunited with Sasha who is the sister of Alone and learns that she is the reincarnation of Goddess Athena. Alone, who is kind, gentle and loves painting was chosen for the body of enemy King Hades. Tenma eventually becomes a saint of Pegasus and engages in a fierce battle with his best friend Alone, the King of Hades. Pegasus Tenma, King Hades, and the Goddess Athena and through the twist of their 3 fates merge together which unfolds a prologue to the original Saint Seiya.

The reunion of Huo Sang plays the tragic song of sin and blood, and the stone spirit is reborn from the desperate situation when the ashes fall.

Set in an alternate version of the Meiji Era, a boy named Sakamoto Ryunosuke returns to Kyoto from Shanghai with his monster (youkai) Nekomaru. The law states that in order to live freely with humans, a youkai must be liscensed. The Kidou Shinsengumi Co. Ltd. is responsible for the capture of unliscensed youkais but must fight with the Tsubamegumi, who resents the new law. It turns out that Ryunosuke is the son of the owner of the Shinsengumis.