Set seven years before the events of the original Saint Seiya manga, the story of Episode G revolves around Athena's Saints, a group of humans with superhuman powers who are devoted to the Goddess of War Athena. Their duty is to protect the world from evil. The protagonist is Leo Aiolia, who is mistrusted by his fellow Saints because of the seemingly traitorous actions of his brother Sagittarius Aiolos in the past. In turn, Aiolia holds a grudge against the Saints as a whole, and against the elite order of the Gold Saints in particular. While Aiolia is sent on mission after mission to prove his loyalty, a modern-day Titanomachy begins as the Titans, ancient gods with a desire for revenge on the Olympian gods, attack the earth.
Tasked with a secret mission by the Oracle of the goddess Athena, Shura travels through time and space to present-day Japan. There, he becomes involved in a bloody war against a group of assassins who are targeting a new reincarnation of Athena. Along the way, he meets fellow Gold Saints who have taken the same journey, but not all of them have come out on the other side as allies.
The world is wrapped in flames and about to be destroyed by the actions of primordial gods intending to cleanse the planet. While the goddess Athena stands alone in a desperate attempt to contain the worst of the attack, it is up to Seiya, the last Saint standing, to battle the gods and join her to save the earth. The final battle of the Gold Saints is about to begin.