Mentre Lady Isabel si prepara per l'inizio della Guerra Galattica, una ragazza di nome Shōko viene attaccata da una Driade, che cerca di trasformarla nella reincarnazione di Eris, la Dea della Discordia. Dopo essere stata salvata da sua sorella maggiore Kyōko, rivelatasi una Sacra Guerriera di Atena, la ragazza viene condotta al palazzo di Lady Isabel.

Shōko viene condotta sul monte Togakushi per allenarsi a diventare una Saintia. Una volta raggiunta la montagna, Shōko incontra il Cavaliere d'Argento della costellazione del Pavone, Mayura, famosa per essere in grado di istruire diversi Saint in tempi record.

The underlings of the evil goddess, Malice Emony and Murder Phonos, plot to take Athena's head to offer it to Eris and raids Saori. Mii stands up against Emony who continues to call Saori an "incomplete god". Shoko's Cosmo flare up during the training with Mayura. Sensing Athena's danger from the Cloth's box, can Shoko ultimately save Saori?.

Shoko succeeded in entering Eris' temple by chasing Phonos who fled battle. As she searches the temple to save her sister, Kyoko, she is informed of a shocking fact by Ate. When Ate's vines catch Shoko off guard and begin to attack, a golden light enwraps her body. To bring back Shoko, Mii heads to Eris' temple and reunites with her where they find Kyoko's ragged body before their eyes.

Kyoko's Cosmo disappeared in the battle at Eris' temple. Saori's heart wavers as she questions her existence from not being able to save Kyoko in defeating the evil god. However, with Saori inheriting Mitsumasa Kido's will, the Galaxian Wars start without mercy. On the other hand, Shoko who was in the hospital had been depressed from Saori telling her goodbye, and she drops the pendant of Pegasus given to her by her sister. The boy who caught it for her was Pegasus Seiya who was entering the Galaxian Wars.

Aphrodite of Pisces takes Athena to the Sanctuary by order of the Grand Master, where both will meet face to face. What secret does the Grand Master hide behind his tears? Meanwhile, Mayura has detected that the remains of Eris are producing an effect that could be catastrophic.

The moment the golden arrow strikes Saori, the Ghosts begin to stir. Shoko who was the evil god's shell had lost conscious, having her soul pulled by the Ghosts. Mayura and the Saintias work hard to calm the evil spirits while Seiya and the Bronze Saints hurry through the Sanctuary to save Athena. Now, the deadly battle of the twelve temples begin.

After the deadly battle, the Saints of the Sanctuary all swear their loyalty to Saori-Athena. Meanwhile, Eris, who was thought to have been sealed, had fused with her host, Kyoko, and multiplied her powers. Saori rises against Eris to protect Shoko, but receives the curse of the apple. The Gold Saints head to the Temple of Eris along with the Saintias to save Athena and to stop the evil god from scattering the Evil Seeds of war that fill people's hearts with hate. That's where Aiolia witnesses his own brother turning his fists against him.

Can you defeat your sister who has fused with the evil god? With Mu's question, Shoko agonizes over the fate she bears. That's when Orion Rigel, the Ghost of an ex-Silver Saint, stands before Shoko. From Rigel's sad eyes that once shared a past with Kyoko during Saint years, Shoko senses his true feelings and - Mii vs. Emony, Aiolia vs. Saga, the individual battles within the Temple of Eris begins.

Finally, Shoko faces the evil god Eris. As Saori's Cosmo grows weaker, all of the Saintias-Shoko, Mii, Xiaoling, Katya, and Erda-put their hearts together to challenge Eris. The Gold Saints continue to protect the Sanctuary as they find out Eris' plan of crashing the temple into it. Aiolia and Milo, who face Saga in a deadly battle, plans to destroy the temple, however - A raging destiny encircles the Saintias, Gold Saints, evil god Eris, and Saori Kido. The final battle begins.