When Seiya, Hyōga and Shun visit Saori (Athena) at the orphanage, they meet an employee called Eri. An orphan herself, Eri takes a liking to Hyōga and one night they sit outside watching the stars. They see a shooting star and Hyōga asks Eri to make a wish. After Hyōga leaves, however, Eri becomes powerfully attracted to the shooting star and wanders alone into the woods, where she finds a golden apple. She is then possessed by Eris, the Goddess of Discord, and kidnaps Athena, planning to use the golden apple to suck her energy out, fully reincarnate and take over the world. Eris leaves a message for the Bronze Saints, who set out for the goddess's temple which appears on the mountains. There, the heroes fight the five Ghost Saints: Maya of Sagitta, Orpheus of Lyra, Christ of the Southern Cross, Jan of Scutum (called by the Japanese name Tateza) and Jäger of Orion.

In Siberia, Hyōga saves a man that is being attacked. Injured, the man manages only to say something about Asgard. Some days later, Saori, Seiya, Shiryū and Shun are wondering about Hyōga and decide to go to Asgard to investigate. At Valhalla, the Lord of Asgard, Dolbar, says he has not heard of any Hyōga and neither has his right hand, Loki. However, at all times Seiya and the others can feel an evil cosmo emanating from Loki and the other Odin Saints called God Warriors. Shiryū, in particular, notices a familiar cosmo coming from Midgard, a mysterious, masked God Warrior. Dolbar makes it clear that he is trying to take control of both Asgard and the Sanctuary, imprisoning Athena in a strange dimension within the giant statue of Odin. Midgard reveals himself as Hyōga and tries to kill Shiryū to prove himself to Dolbar. Thus, it is the task of the Bronze Saints to defeat Dolbar, Loki and the rest of the God Warriors, to save Athena and Hyōga.

After the bloody battle against Hades, the goddess Athena and her saints are still recovering when they find themselves face to face with their newest and most formidable foe: the dreadful moon goddess Artemis. Artemis replaces Athena as the earth guardian deity and takes over the Sanctuary, turning Athena's Saints into her servants. Upon invading the Sanctuary, the Bronze Saints learn that Athena was banished by Artemis and decide to fight the moon goddess in order to rescue their true goddess and free the Earth from Artemis's ominous control.

The plot involves the coming of Lucifer to the Sanctuary, where his underlings systematically dispose of the surviving Gold Saints. Athena goes to Lucifer to ask for peace, placing herself in peril. The Bronze Saints must then come to her rescue, destroying Lucifer's Fallen Angels (Seima Tenshi in Japanese) in the process.

Athena receives the visit of Phoebus Abel, her older brother and God of the Corona. He informs her that he has come to destroy humanity as punishment for their corruption, just as it was done in ancient times. He dismisses Seiya and the Bronze Saints, as she will now be guarded by Abel's three Corona Saints, Atlas of Carina, Jaow of Lynx and Berenike of Coma Berenices, and the five resurrected Gold Saints who died in the Sanctuary battle: Saga of Gemini, Deathmask of Cancer, Shura of Capricorn, Camus of Aquarius and Aphrodite of Pisces. When Athena rebels against Abel's plan, he attacks her, sending her soul to Elysion, the final resting place from which there is no return. The Bronze Saints immediately rush to the Sanctuary to save her and ultimately overcome Abel.

Warriors called "Saints" are the champions of hope who have always appeared since the Age of Myth whenever evil threatens the world. In this present day story, many years since the long fought "Holy War" we find Saori Kido, a girl troubled by her mysterious powers. She is saved by a boy, Seiya "Bronze Saint" from a sudden attack by an assassin, through the accident Saori realizes her destiny and mission and decides to go to "Sanctuary" with Seiya and his company of Bronze Saints. In Sanctuary they confront "Pope" and wage a desperate battle against the greatest Saints, the "Gold Saints".