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In 1990, in Elysion, the five Bronze Saints, Seiya, Hyoga, Shun, Shiryu and Ikki, wreak havoc in the Underworld’s army and engage the god Hades in a battle to the death. Hades remembers then that he has seen Seiya before and concludes that they have fought 247 years prior, in the 18th century. The Pegasus Saint of that era is an orphan who is best friends with Alone, the host of Hades. Meanwhile, Bronze Saints Dohko and Shion are promoted to Gold Saints and the two duos meet at the start of the 18th century's Holy War.
Hakuo Gakuin used to be a prestigious high school and was famous for martial arts. However, because its rival school, Seishikan, has been cowardly luring its superior students, Hakuo is declining. In order to recover from the situation, the acting principal of Hakuo, Hojo Himeko, sends Yagyu Ranko to Fuma Village in search of the famous Fuma ninja clan for assistance. The leader of Fuma sent Kojiro to Hakuo. There he faces the notorious Yasha clan, who fights for Seishikan, led by Asuka Musashi. Soon Kojiro's comrades arrive and an all-out ninja war postponed for 500 years begins between the two clans.
A series of side stories focusing on each of the Gold Saints from Saint Seiya: The Lost Canvas exploring their lives, mostly events which occurred before those of Saint Seiya: The Lost Canvas.
Spinoff of Saint Seiya: Saintia Shou.