A comet burns in the sky, its brilliant light shining down upon the people of Earth. At that time, a giant army of viruses invade the real world, crushing everything in their path. Netto and Enzan use cross fusion to intervene, but are whisked away to an unknown location, only to be confronted by the one responsible for the attack - Duo!

Eris is the goddess of chaos and uses the body of Elien, who is a friend of Hyoga, to revive herself. She obtains the golden apple to drain Athena's life energy to make her ressurection complete and to be able to turn the world in a place filled with chaos. But to be able to attack Eris, Seiya and his friends will first have to defeat the Ghost Knights.

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.

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.