It has been 243 years since the previous Holy War between Athena and Hades, God of the Underworld. On a tower that Roshi has been observing, the seal Athena placed ages ago has lost its effect. The spirits of the 108 Specters, Hades' soldiers, are now free. At the Sanctuary, Nachi, Ichi and Shaina notice that graves from the Saints' graveryard have been disturbed, with the bodies coming out from the inside. At the House of Aries, a shadowy figure approaches Mu, who seems familiar to him. He orders Mu to bring him Athena's head in 12 hours. When he refuses, two more figures appear. Two Gold Saints whose lives were lost in the Battle of the 12 Houses, Cancer Deathmask and Pisces Aphrodite. Since they sold their souls to Hades, he offered them new lives, bodies, and Surplices, armors from the Underworld, resembling their Gold Cloths.

The shadowy figure deduce that Mu teleported Seiya instead of destroying him. Mu blocks Deathmask and Aphrodite's paths once more and defeats them with Starlight Extinction. At Lushan's Waterfalls, Roshi tells Shunrei he is leaving and might never come back, telling her to not let Shiryu leave her side and wishing Seiya and the others would live peacefully as normal teenagers after fighting for so long. As Roshi leaves, three shadowy figures approach Shunrei. Deathmask and Aphrodite have been vanquished, but three more figures approach Mu. Shaina orders Nachi and Ichi to set fire to the remaining graves, while Jabu discovers that three more Gold Saints were revived. At Lushan, the figures ask Shunrei for the whereabouts of Shiryu and Roshi, but Shiryu, still blind, comes to her rescue.

At Hades' castle, Wyvern Rhadamanthys, one of the three judges of the Underworld, begs Pandora, a beautiful girl and Hades' representative, to give him permission to go to the Sanctuary, but she refuses, and says the revived Gold Saints will handle the mission of killing Athena. Mu heads for the House of Taurus to find Aldebaran. Shun awakens after he keeps having dreams of a girl who resembles Pandora. Sensing something is wrong, he heads towards the Sanctuary. Tatsumi, under Saori's orders, tries to keep Shun from leaving, but to no avail. Mu finds Aldebaran, but the Taurus Saint has died, and only his Gold Cloth and a small trace of his Cosmos remain. The one responsible emerges from the shadows, a Specter, Deep Niobe, who was sent by Rhadamanthys. Deathmask and Aphrodite invade Hades' Castle, hoping to see the god, but Rhadamanthys sends them to the Land of Death. Rhadamanthys appears before them and tosses them into Yomutsu Hirasaka. Niobe uses his Deep Fragrance, which killed Aldebaran, against Mu, but the Crystal Wall blocked it. Mu claims that Niobe has already died, due to Aldebaran's Great horn, only it was delayed. As Mu leaves, Niobe's body is crushed. Aldebaran's Cosmos was able to save Mu, and he claims his death was not in vain. Shun heads for a ship that will take him to Greece, but is attacked by Canis Major Sirius, Heracles Alghetti, and Musca Dio, who have revived. Shun, with his damaged Andromeda Cloth, kills all three Silver Saints with his Nebula Chain. Mu heads for the House of Gemini, but is surprised to sense two powerful Cosmos coming from it. Saga tells Camus and Shura to keep going, while he fights the new guardian of the House.

Right before everyone's eyes, Aldebaran, Saga, Deathmask, Aiolos, Shura, Camus and Aphrodite came back to life. Friends and comrades happily reunite, (Aiolos with Aiolia; Camus with Hyoga; Shura with Shiryu; Aldebaran with Seiya; Deathmask and Aphrodite with Mu. Also, Kanon's soul unites with Saga) but the reunion is short lived. Aiolos pulls out an arrow, preparing to fire it at the wall. Aiolia says goodbye and warns the Bronze Saints to leave. Dohko says all 12 Gold Saints will focus their Cosmos to Aiolos' arrow in order to destroy the wall, but it will cause an explosion so intense, that the Gold Saints will lose their lives. He explains that no human can reach the Elysium Fields, but the Bronze Saints can since their Cloths are bathed in Athena's blood. Dohko says that Hades cares a lot about his body and keeps it sealed in Elysium, which is why he possesses a human whenever he revives. Finally, he orders them to destroy Hades' body, which will end the Holy Wars between Athena and Hades, forever. The 12 Gold Saints bid a heartbreaking farewell to the four Bronze Saints. Seiya and his friends, with tears in their eyes, bid farewell to the brave soldiers who taught them so much and escape. Dohko reminds Shiryu that Shunrei prays for him and Shura reminds him of their battle and to remain strong. Camus reminds Hyoga of their battle and assures him he can win. Aphrodite also reminds Shun of their battle and believes he will make a miracle. Minos confronts the Bronze Saints and easily blocks their attacks. The 12 Gold Saints entrust the Earth, Athena and the future to the Bronze Saints as Aiolos fires the arrow, and causes a monstrous explosion, destroying the Wailing Wall. Minos is caught in the blast, seemingly defeated. Seiya and his friends rush back inside, seeing the Gold Saints have opened a path through the wall. But the Gold Saints have died, only the 12 Gold Cloths remained. Their spirits bid farewell to the Bronze Saints, reminding them to stay strong, fight for justice and never lose hope. Having mourned the Gold Saints' deaths, Seiya and his friends head towards the Elysium Fields to hand Athena her Cloth, destroy Hades and stop the Grand Eclipse. Saori is then shown trapped in a giant urn, turning red at the bottom. Ikki also heads towards the Elysium Fields, with Pandora watching him, remembering her childhood.

The Bronze Saints head to the Elysium Fields, but Shiryu stays behind, sensing the presence of Specters. Three of them appear, Alraune Queen, Minotauros Gordon and Basilisk Sylphid. Shiryu fights them all at once, unleashing the force of Excalibur. Seiya, Hyoga and Shun reach the other side of the Wailing Wall, but find an inter-dimensional path of time and space. At the end of the path is a shining light, leading to the Elysium Fields. Minos, having survived the blast, catches up to them, with Hyoga staying behind to fight him. Hyoga makes an ice barrier while Seiya and Shun go forward. Minos breaks the barrier and uses Cosmic Marionation on Hyoga. Seiya is being dragged by the pressure of time and space, but then his Cloth grows wings, due to Athena's blood. He rescues Shun and both head to the Elysium Fields. Hyoga freezes the threads of the Marionation, immobilizing Minos and attacks with Aurora Execution. Minos barely survives and traps Hyoga with a remaining thread, but he is suddenly destroyed due to the dimensional pressure, proving only gods can walk the path. Hyoga and the others were spared because of their Cloths bathed in Athena's blood. Shiryu holds his own against the three Specters, taking their attacks head on and still fighting. He challenges all three to attack him at once and kill them with his master's technique, One Hundred Dragons. With the pressure of the techniques, Shiryu flies all the way to the inter-dimensional path, where Hyoga is waiting for him. Sylphid somehow survived and goes after Shiryu but he is also destroyed by the pressure. With his Cygnus wings, Hyoga takes Shiryu to the Elysium Fields. Meanwhile, Seiya has successfully made it and wakes up in a utopian paradise.