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.

The clash of the forbidden techniques are felt throughout the entire Sanctuary and are evenly matched, increasing its destructive force. Suddenly, Seiya, Shiryu, Hyoga and Shun burn their Cosmos to push back the techniques towards Saga and his group. Then they surround the exclamtions in order to stop them. The four Bronze Saints awaken their Seventh Sense, their Cloths turn golden, and they unleash their techniques, forcing the exclamations into the sky where it explodes. However, Seiya and his friends are caught in the disaster as the House of Virgo crumbles from the impact. At her Temple, Saori has Kanon retrieve something from the Pope's chambers, left by Saga 13 years ago. Mu, Aiolia and Milo emerge from the rubble, wondering where the Bronze Saints are. Saga, Camus and Shura also emerge from the wreckage. Saori has the Gold Saints bring Saga and his group to her Temple. Seiya and his friends awaken, having survived the commotion. They head for Athena's Temple as well. Once Saga and the others arrive, Kanon hands him a chest, with a golden dagger inside. Thirteen years ago, Saga, disguised as the Pope, tried to kill Athena with the same dagger as a baby. Saori tells Saga to kill her with the dagger, to free them from their suffering. Seiya and his friends arrive, but are too late as Saori kills herself. Back at Hades' Castle, Wyvern Rhadamanthys is informed about Athena's death, and is punished by Pandora for sending Specters to their deaths. Seiya and his friends mourn Saori's death, but Shion arrives, saying the real battle will soon begin. The four Saints attack at the same time, but Shion tosses them aside and is about to explain the whole truth, and the reason behind Athena and Shaka's deaths.

Shion reveals that the Gold and Silver Saints revived by Hades never betrayed Athena and would never hurt her. He also shows the Bronze Saints the reason why they went through all this trouble. He uses Saori's blood and it flies towards Athena's statue. It begins to glow and then shrinks down to a tiny version of itself. Shion explains that the statue is really the Athena Cloth, which needs her blood to awaken. Shion was the only one who knew the secret. If Saori plans to win against Hades, she needed her Cloth. In the Underworld, Hades came to Shion and the other Saints, revived them and offered them a deal: if they killed Athena in 12 hours, they would be granted eternal life. They pretended to accept the deal, to enter the Sanctuary and get her blood for her Cloth, so Athena would defeat Hades. Shion gives the Bronze Saints the following order: go to Hades' castle and destroy him. At Hades' Castle, Saga and his group take Saori's body covered in a sheet to Pandora, but the sheet is revealed to be empty, and they are there to find Hades and kill him. Shion's 12 hours are almost up and will return to the Underworld soon. He gives the Saints Athena's blood to revive their heavily damaged Cloths. Now, with their Final Bronze Cloths, Shion entrusts the Seiya and his friends with Athena's Cloth to make sure Saori receives it. Aiolia, Mu and Milo arrive at Hades' Castle and face Rhadamanthys, but for some reason, they can't defeat him, and the Specter picks them apart, with no effort at all. Shura is about to cut Pandora, Camus freezes a Specter, Frog Zeros, and Saga asks Pandora to take them to Hades. But they are weakened, because their 12 hours are almost up. Pandora demands to know where Athena is, and Saga tells her that she is in the Underworld. Pandora realizes that Saori plans to fight Hades. Rhadamanthys is about to toss Aiolia into the Underworld, but Shun's chain rescues him. The four Bronze Saints have finally arrived.

Aiolia, Mu and Milo sacrifice themselves, stalling Rhadamanthys, allowing the Bronze Saints to find the room where Saga and his group is. The Gold Saints are tossed into the Underworld, presumably losing their lives. Saga and the others' 12 hours are up and the Bronze Saints mourns their deaths after receiving some timely advice before disappearing. Hyoga kills Zeros, because he was stomping Camus, with the Aurora Execution. Just as they spot Pandora, who is going to the Underworld, and try to go after her, Rhadamanthys appears and gains the upper hand on the Bronze Saints. Seiya gets up again, struggling to attack Rhadamanthys. As the Specter is about to toss Seiya down to the Underworld, Shiryu, Hyoga and Shun attack at the same time, but he knocks them down again with his Greatest Caution technique. The Bronze Saints struggle to get up, remembering the words of the Gold Saints and fight back. Rhadamanthys attacks again and Seiya faces him once more. With his Comet Punch, Seiya is able to damage his Surplice. Seiya's Cloth turns gold and he and Rhadamanthys fall down into the Underworld. As the sunrise gets closer, Dohko and Shion contemplate the fact that the Bronze Saints are fighting again. Shaka's message was actually a way to reach the Underworld, alive, which is where he and Saori are right now. Shion, confident that the Bronze Saints will awaken the Eighth Sense, based on the miracles they have achieved in the past, says goodbye to his old friend Dohko and disappears. He and Kanon head towards Hades' Castle. Shiryu, Hyoga and Shun burn their Cosmos, hoping to reach the Underworld alive. Seiya heads to the Underworld, hoping to reach Saori.

Seiya and Shun reach the First Prison and encounter Markino, a skeleton that leads them to Balrog Rene, who judges the dead and sends them to their appropriate hell. Markino is then killed by Rene, using his Fire Whip, because of him not being quiet. Rene proceeds by showing Seiya his past crimes during his life with Reincarnation. Seiya is shown childhood memories, and the opponents he has defeated. He then tries to explain his actions, but Rene ignores him and sends him to the First Valley of the Sixth Prison, where people who have use violence against others in their lives boil in a lake of boiling blood. Shun rescues him, however Rene notices something strange about Shun. Shun tries to justify the actions of humanity, but is sliced to pieces with the Fire Whip. Rene is then scolded by Hades for cutting his body. In panic, he searches for the body, but Rhadamanthys appears, pointing out it was an illusion. Seiya and Shun are fine, wondering what happened. Rene discovers who made the illusion, Gemini Kanon, who wanted Rene to lead him to Hades. Kanon then destroys Rene with no difficulty and confronts Rhadamanthys about why he defeated Aiolia, Mu and Milo so easily, because of a barrier at Hades' castle that lowered their strength to 1/10. Seiya and Shun arrive, but Kanon attacks them, reminding Shun to be stop being sentimental, in order to save the innocent. He then tells them to go find Athena. Rhadamanthys attacks Kanon, but he counters with the Imperial Satanic Illusion to control him and kill Hades. He is interrupted by Specters who tell Rhadamanthys that Pandora wants to see him. As the Judge leaves, Kanon destroys the lower Specters with Galaxian Explosion.

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.

The five Gold Saints burn their Cosmos and toss the weapons into the Wailing Wall, but are ineffective and come back to them. Shaina gathers with Jabu and the other Bronze Saints. Marin and Kiki arrive as well, deducing that chaos is occurring around the world, due to the Grand Eclipse. Seiya takes one of the weapons and attempt to destroy the Wailing Wall, like he did with the Main Breadwinner in Poseidon's Sanctuary, risking his life. Out of nowhere, a light appears. At the Sanctuary, lights coming from the Houses of Taurus, Cancer, Sagittarius, Capricorn, Aquarius and Pisces head towards the Underworld. Hyoga and Shiryu have made it through the last Prison and notice the lights headed toward Giudecca. The lights are the souls of the deceased Gold Saints and their Gold Cloths. All Gold Cloths have gathered in the Underworld, resonating with one another. Kanon removes his Gemini Cloth, sending it to Giudecca, and fights Rhadamanthys again, however, he seems to be at a disadvantage. Kanon takes a hold of Rhadamanthys and as they rise farther into the sky, he uses a final Galaxian Explosion, destroying them both. He then bids farewell to Athena and his brother, Saga. Hyoga and Shiryu make it to the Wailing Wall and see all 12 Gold Cloths in one place. Suddenly, the empty Gold Cloths come apart and begin to take shape.