Sun God Apollo the brother of Athena is here to take Athena back to heaven and taking over the sanctuary. He revived the deceased gold saints and use them and a few god saints as bodyguards. But Athena did not obey him, Apollo had no choice but send her to hell. On the otherhand, the bronze saints are on their way to save Athena.

From the dawn of time, there have been warriors who protected the Goddess Athena. Once forces of evil appear, these warriors, called the Saints will present themselves. A young woman, Saori Kido, learns about this force known as "Cosmos" and that she is the reincarnation of Athena, protector of love and peace on Earth. However, the Pope of the Sanctuary, who is in the charge of all the Saints, does not take kindly to Saori, and targets her for usurping the identity of Athena. An assassin is sent out to kill her. Fortunately, one of the Bronze Saints, Seiya, manages to protect her. But will Seiya be able to protect Saori through to the end in the gripping saga of Saint Seiya: Legend of Sanctuary?

After the Saints' victory against Hades, Seiya is left wounded and motionless in a wheel chair with no possible chance of recovery. Athena's sister Artemis, the Virgin Goddess of the Moon and twin sister of Apollo, makes an elaborate proposal - to restore Seiya's physical health in exchange for the supremacy of Sanctuary. Athena accepts and Artemis and her "Knights of the Sky" swiftly take control of Sanctuary. Now Seiya and his fellow Bronze Saints combat the forces of Zeus to regain their homeland but it will not be so easy. Bronze Saints Hydra Ichi and Unicorn Jabu, and Silver Saint Ophiuchus Shaina have join forces with Artemis and Apollo.

Lucifer has been awoken from his eternal slumber by the spirits of Eris, Abel and Poseidon. He has come to kill Athena and fulfill his heart's burning desire: becoming the strongest of all the gods.