Orphée plays his Death Trip Serenade, making Pandora and the three Judges fall asleep. Before he can attack Hades, Rhadamanthys strikes Orphée, knowing he would betray them. Seiya and Shun emerged from the trunk unscathed and attack the Judge. Hades appears, wearing Shun's pendant, and Hades's face looks exactly like Shun's. Orphée attacks with Stringer Fine, with Hades seemingly destroyed, but it is revealed to be a fake body. Rhadamanthys strikes Orphée's heart, ordering him to awake the other Judges and Pandora. Orphée, dying, tells Seiya to attack them both while he holds Rhadamanthys. Seiya awakens his Eight Sense and attacks with his Meteor of Pegasus. As Orphée dies, he entrusts the Bronze Saints with Athena. Rhadamanthys survives the attack, but Shun begins to act like Hades and his hair turns red. Seiya tries to snap him out of it, but Hades has taken over his body. Rhadamanthys attacks Seiya, defeating him. Both Seiya and Orphée's bodies are taken to the frozen hell in the Eighth Prison, Cocytus, where the dead who have committed crimes against the gods, are buried up to their heads. Pandora and the Judges awaken, and Hades sits on his throne. The Judges find it hard to believe the God of the Underworld used to be a Saint. Hyoga, Shiryu and Kanon arrive at a swamp in the Fourth Prison, guarded by Lycaon Phlegyas. Hyoga and Shiryu are defeated by him, but Kanon kills Phlegyas with his Galaxian Explosion. He takes the raft and the unconscious Saints with him to the Fifth Prison. At the Eighth Prison, Pandora tends to Hades' wounds from her spear, trying to find them in the trunk. She then calls him her younger brother.

Shiryu and Hyoga recover as they reach the Fifth Prison, where the dead are forever burning. They encounter Kanon as he kills a giant Specter. Rhadamanthys arrives and tells the Saints about Seiya's defeat and Shun becoming Hades. Kanon tells Hyoga and Shiryu to continue while he fights Rhadamanthys and gains the upper hand. Suddenly, Aiacos and Minos come to kill Kanon and attack with their Galactica Illusion and Cosmic Marionattion, respectively. However, the strings from the Cosmic Marionattion are suddenly cut, releasing Kanon. Just then, with his Final Cloth, Phoenix Ikki arrives. Kanon tells him that Shun is Hades, but Ikki doesn't believe it. When Ikki hears Pandora's name, though, he remembers that when he and Shun were children, Pandora, as a child, tried to take Shun from him, saying his body belongs to Hades. He hadn't seen her for years after that. Ikki is distracted and gets attacked by Aiacos. He then gets up, in tears, realizing Shun is going to sacrifice himself. After accepting his challenge, Aiacos sends Ikki flying with his Garuda Flap twice. On the second time, however, Ikki manages to knock down Aiacos. Back on Earth, Eagle Marin encounters a mysterious, but familiar young girl.

Aiacos recovers and attacks Ikki with Galactica Illusion. At Giudecca, Hades and Pandora sense Ikki's powerful Cosmos. He asks Pandora to bring him before his throne. Ikki gets up and uses the Phoenix Illusion, with Aiacos seeing his own death in his head. Aiacos is then finally killed by Ikki's Flying Phoenix. Shortly after his victory and before he is able to challenge the two remaining Judges, Ikki is surrounded by a strange light and disappears. Pandora teleports Ikki to Giudecca. He is surprised to see his brother as Hades. Pandora reminds Ikki of when they first met, when he almost lost his life protecting his baby brother. Pandora, holding what looked like the Universe in a mantle, tried approaching the baby Shun, but a powerful Cosmo kept her at bay. Not willing to risk Shun's body, Pandora gives Shun the pendant seen earlier, and takes her leave. In the present, Ikki finally remembers everything. The pendant, which reads "Yours Ever", was from Hades, who chose Shun to be his vessel. Ikki destroys the pendant and knocks Pandora out of the way. He goes to his brother and tries to snap him out of it. Hades pushes Ikki back and reveals his plan, the Grand Eclipse. His plan is to align all the planets in the Solar System, blocking the Sun from the Earth. This eternal eclipse will cause Earth to undergo a new Ice Age, becoming a world of death. Ikki attacks Hades numerous times with a strengthened Cosmo which destroys most of the throne room, but his attacks are easily returned by the God. Suddenly, Hades begins strangling himself. Shun's spirit appears behind Hades and tells Ikki to destroy Hades once and for all.

Ikki realizes that Shun allowed Hades to enter his body, to have the chance and sacrifice himself, like his constellation of Andromeda, to end the battle. Pandora tries to stop Ikki, but the Nebula Chain surround Ikki to protect him, giving him the opportunity to strike. Shun tells his brother not to worry, and that he is happy giving up his life if it means saving others. All the Saints in the Underworld sense Ikki's Cosmo. Ikki pierces Shun's chest and extracts Hades' soul from his body, destroying it. Suddenly, Hades' real soul emerges from Shun's chest, but it was all a dream in Seiya's head. In reality, Ikki had actually stopped his attack, injuring his fist in the process. Then Hades' hair turns from red to black, meaning he now has complete control over Shun's body. He then defeats Ikki with no effort. Pandora orders Harpy Valentine to bury Ikki at Cocytos and leaves Hades to be alone. Just then, Shaka appears, ready to kill Hades. Valentine buries Ikki in Cocytos, filled with Saints who lost their lives in the previous Holy Wars. Seiya discovers Aiolia, Mu and Milo are also buried here. He then asks Valentine to release him, informing him that he has Athena's Cloth. Valentine releases Seiya and is able to dodge his attacks. Seiya is knocked down and gets up again, but Valentine strikes back with his "Greed the Life" technique. Shaka prepares to strike, but Saori arrives.

Seiya still struggles against Valentine, who attacks him again. The Specter tries to retrieve Athena's Cloth, but Seiya keeps him from taking it. Athena's Cosmo awaken Seiya and he stands to fight again. Meanwhile, Saori begs on her knees and asks Hades to stop the Grand Eclipse, but he refuses, yet Saori is willing to give up her life. Hades gives Shaka Pandora's trident, and orders him to kill Athena. But Shaka throws it at Hades, although Saori stops the trident. Hades points the trident at Shaka, but she stands in his way. Seiya and Valentine charge at each other, Seiya killing the Specter with his Meteors of Pegasus. Saori stops the trident, and bleeds. She burns her Cosmos and as the blood touches Hades and hurts him, his hair color is changing back to red and then to green. Hades' soul escapes Shun's body and charges at her. Saori strikes him with the trident, stained with her blood. However, Hades attacks her and both gods disappear. Shiryu and Hyoga kill multiple Specters on their way to the Eighth Prison and sense Athena's Cosmos disappearing. Pandora, Kanon, Rhadamanthys, Minos, Dohko and Seiya also sense Hades and Athena's Cosmos disappearing.

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.