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.

Scorpio Milo arrives at Athena's Temple, sensing an enemy, but Saori assures him that the person is an ally, and is protecting the House of Gemini. Saga recognises the new guardian, remembering all of his atrocities, his brother Kanon, who survived the battle of Poseidon and now wearing the Gemini Gold Cloth. In Siberia, Hyoga decides to never see his mother again, even though he will never forget her. He remembers Camus' teachings and the influence he had on his life. Suddenly, three figures approach him. Kanon says that Athena has cleansed the evil in his heart and has forgiven him. He also says that he will fight for justice from now on. Even though Shura and Camus went ahead, they are caught in the Gemini Labyrinth. Saga attacks, but the Gemini Cloth is empty. He then fires a huge blast of energy, all the way to the Pope's chambers, striking the real Kanon. Milo appears, and believing Kanon is still a threat, orders him to leave, acknowledging the remaining Saints will never forgive him for all he's done. Kanon refuses, saying he fights for Athena. Milo retaliates with his Scarlet Needles, one after another. Meanwhile in Siberia, the Silver Saints Lizard Misty, Whale Moses and Centaurus Babel, revived by Hades, fight Hyoga and are quickly defeated by his Aurora Thunder Attack, with Babel asking him to save Athena. Kanon refuses to fight, and is willing to receive all of the Scarlet Needles, since Saori has forgiven him. Saori asks Milo to stop what he's doing, but he won't because of the evil Kanon has done. Kanon received 14 Scarlet Needles and begins to bleed profusely. Milo uses Antares, the final needle. Milo takes his leave to the House of Scorpio, but before leaving, he admits that Kanon is now their ally, and instead of using Antares, he stopped the bleeding. The Scarlet Needles were a test to see if Kanon was telling the truth. With the illusions gone, Shura, Camus and Saga emerge from the House of Gemini. Saga, with tears of joy, hoping that his brother really became a guardian of justice, heads with his friends to the House of Cancer.

As they approach the House of Cancer, Saga, Shura and Camus can sense the presence of death, and end up in the Land of Death. Suddenly, zombies start attacking them. Shiryu finally arrives at the Sanctuary, but is attacked by someone. Saga defeats the zombies and stops the illusion with his Galaxian Explosion. Shura senses someone following them, but Saga said they will take care of them later. At the same time, Ikki appears before Shiryu, telling him to leave as they aren't allowed here, and that he's only here to observe the battle. Angered, Shiryu attacks Ikki, saying he's fighting for Athena and his friends. Ikki then points Shiryu to Seiya's direction before leaving. Shion and Dohko talk, revealing that they were the only survivors of the previous Holy War. Shiryu finds Seiya, alive, at the colisseum, due to Mu's teleportation. Even though Seiya is angry at Ikki for not joining them now, Shiryu reminds Seiya that he is their friend and comrade, and that he may be needed in this battle. Both friends head to the 12 Houses, reminiscing about the past when they last ran up those stairs to save Athena. Meanwhile, Saga and his friends are still trying to break through the House of Cancer, sensing a powerful Cosmos, belonging to Virgo Shaka, who was using an illusion to distract them for 12 hours. Saga realizes he must kill Shaka to stop the illusion and fires a powerful blast to the House of Virgo. However, Shaka protected himself with a barrier, and counters with a blast of energy, just as powerful to the House of Cancer. Shion tries to leave, sensing the attacks, but Dohko stops him, ready to settle the score.

Shion and Dohko's power clashes, but it seems Shion has the upper hand, due to Dohko's current appearance. Feeling this, Shiryu tells Seiya to go ahead while he goes to help his master. Dohko orders Shiryu to leave and attacks Shion with the One Hundred Dragons. Hyoga and Shun arrive at the Sanctuary, but Shaina stands in their way. Dohko's dragons are no match for Shion who counters with his ultimate attack, Stardust Revolution. Shiryu wears his damaged Dragon Cloth and attacks Shion. Shun understands why Saori gave the order, but he realizes they must protect her no matter what. Shaina prepares to battle Hyoga once he starts burning his Cosmo. At the House of Aries, Shion blocks the Rising Dragon, but Dohko gets up and asks Shiryu to leave. However, Shiryu can't leave, knowing his master is fighting alone. Dohko agrees to let him stay, promising to apologize to Athena later. Hyoga prepares to attack, but Shaina turns her back and allows them to move forward. Shion attacks, but the Libra Gold Cloth saves Dohko and Shiryu. Suddenly, Dohko burns his Cosmos, and reveals something amazing. His body starts to crack like a shell, and a younger body emerges from the old one. The young Libra Dohko has returned. He reveals that Athena gave him the gift of Misopethamenos, which allowed him to stay young, meaning, since 243 years passed, for Dohko, it was only 243 days. Dohko tells Shiryu to follow Mu and defeat the Specters that came to the Sanctuary. Dohko dons his Cloth after 243 years and prepares for battle. Shion and Dohko clash with their ultimate techniques, Stardust Revolution and the One Hundred Dragons. Shiryu is sent flying due to the impact. Seiya, Mu, Hyoga, Shun and Shiryu sense both Shion and Dohko's Cosmos have disappeared.

Mu arrives at the House of Cancer, destroyed by Shaka's attack. He is then bound by psychokinesis, and a group of Specters make themselves known, searching for Saga, Camus and Shura. Cyclops Gigant tries to attack Mu, but Seiya arrives in time to save him, asking Mu to let him and his friends participate in the battle. Gigant avoids his Meteors and strikes multiple blows. Then, a strange, slimy creature, who used the psychokinesis, named Papillon Myu tells Gigant and the other Specters to head for the House of Leo. Shiryu encounters Hyoga and Shun, wanting to know where his master is, but there was no trace left, so they continue on their way. Mu is freed from the psychokinesis, because Myu wants to fight him. Myu attacks with Ugly Eruption, but Mu counters with Crystal Wall and Stardust Revolution. Myu then turns into a huge insect and uses Silky Thread to bind Mu and Seiya. Shiryu, Hyoga and Shun pass the House of Cancer, not realizing their friends were trapped close by. Mu and Seiya emerged from the cocoons and find another one above them, with Myu inside. He then emerges in his ultimate form and attacks Seiya with his psychokinesis, but the voice of his friends allow him to break free, much to Myu's shock as not even Mu could do that. Mu then tells him to go to the House of Leo, while he fights Myu. Mu dodges Myu's Fairy Thronging and traps the fairies and him with Crystal Net. Myu is then killed by the Starlight Extinction. After defeating his opponent, Mu heads for the House of Leo.

Seiya meets up with his friends and they head to the House of Leo. Meanwhile, Gigant and his group of Specters encounter Aiolia at the House of Leo, still searching for Saga and the others, since they were suspicious of them. Five Specters try to get through the House, but Aiolia quickly eliminates them with his Lightning Plasma. Another Specter, Worm Raimi, appears. Seiya and his friends encounter three dead Specters, without their Surplices. One was frozen to death, one was slashed in the back, and the last one had major burn marks. They continue towards the House of Leo. Raimi tells the other Specters to go to the next House and digs a hole underground. Aiolia senses familiar Cosmos within the Specters. Suddenly, he is bound by Raimi's tentacles, but frees himself and drags Raimi above ground. Aiolia attacks but the Specter goes underground and reemerges. However, Aiolia finishes him off with a Lightning Bolt. The four Bronze Saints arrive and tell Aiolia about the dead Specters. Gigant and the other Specters arrive at the House of Virgo and find it in shambles. Shaka appears before them and blocks their attacks with his barrier. He then pulls out a rosary with 108 beads, the same number as Hades' Specters. When a bead turns black, it means a Specter has died. So far, 11 Specters have died, but Gigant is confused, there should only be 8 dead. Shaka attacks the Specters, but three of them stop the attack and use Diamond Dust, Excalibur and Galaxian Explosion. Shaka is able to block the techniques, but just barely. Knowing who the three Specters are, Shaka removes the Surplices to reveal Saga, Camus and Shura. Aiolia tells Seiya and the other Saints that Shaka is willing to sacrifice himself.

Shaka questions Saga about his true intentions, and they tell him that they are going to kill Athena, so he lets the three of them go to the next House. Shaka then kills the remaining Specters, even though they believe Hades will grant them eternal life, but Shaka proves them wrong. He then stops Saga and the others to try to get the real truth out of them, now that they aren't being followed. However, they still plan on killing Athena. Shaka leads the three former Saints to a garden known as the Twin Sala, also known as Buddha's final resting place. Shaka fights all three of his former friends at once and seems to have the upper hand, but can't keep up for long. He then uses his most powerful technique, Heaven's Treasure to eliminate his enemies' five senses. Unless of course, they use a technique forbidden by Athena since ancient times, the Athena Exclamation. The technique can be used by three Gold Saints, and has the same power as the Big Bang that created the Universe. As they lose their senses, Saga and the others ponder about using the technique, facing eternal shame. Saga convinces them otherwise and reminds them why they allied themselves with Hades. Seiya, Aiolia and the other Saints arrive at the House of Virgo, but Mu blocks the door of the Twin Sala, telling them Shaka wants to die. Shaka is about to eliminate the final senses, but Saga, Shura and Camus use the Athena Exclamation to kill him. While receiving the technique, Shaka remembers Buddha's teachings, while Athena and the other Saints sense and mourn his death.

Saga, Shura and Camus only have one of their senses each, but Shaka has survived somehow. He sits under the Twin Gala and writes a message with his blood on flower petals, then the wind blows them towards Athena. Saga and the others realized that Shaka's spirit had come back, just to write his message. After mourning Shaka's death, Saga and the others encounter the Saints, but Aiolia attacks all three, wanting to avenge Shaka. However, Saga blocks his Lightning Plasma. With only four hours left, the former Saints are willing to see Athena no matter what. Meanwhile, Saori receives the flower petals with Shaka's message. The message read Arayashiki, and Saori understands the meaning behind Shaka's death. Milo arrives at the House of Virgo, attacking Saga and the others, but Saga counters with Galaxian Explosion. Saga, Camus and Shura get into position for the Athena Exclamation. Mu, Milo and Aiolia also get into position to use the same technique, despite the protests of Seiya and his friends. If two Athena Exclamations clash, their destructive power will increase to infinity, destroying the entire Sanctuary. As the Gold Saints entrust the Bronze Saints with Athena, the Athena Exclamations are unleashed at the same time.

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.

Shiryu, Hyoga and Shun are about to jump into the hole leading to the Underworld, but Dohko stops them, warning them that only Specters will be able to reach that world alive. He also tells them that they must reach Arayashiki, known as the Eighth Sense. Shaka and Athena had reached this sense by being as close to death as possible, to reach the Underworld alive. Dohko and the Bronze Saints, thanks to their previous battles, awaken the Eighth Sense, and land in the Underworld. Seiya has made it as well, reaching the Eighth Sense beforehand and encounters Shun. Now they must find Saori and give her Cloth to her. Seiya and Shun reach the Acheron River, and see dead people who lived their lives in apathy and aren't allowed to cross the river. A boat comes with a Specter, Acheron Charon, who guides dead people across the river. He begins to fight the Saints, but offers them a ride in exchange for money. Shun offers Charon a golden pendant, something he has had since he was a baby. Even though Charon says it isn't enough, he gives them a ride. At the halfway point, Charon knocks Seiya off the boat where he is being dragged to the bottom by dead people who tried to swim across. Shun saves Seiya and he attacks, breaking through Charon's Rolling Oar defense. The Specter falls into the water, asking for help since only he knows the way to the other side. Shun helps him, but Charon attacks Seiya with Eddying Current Crusher. He then attacks Shun, but looks at his pure eyes, being aware of his pure heart and stops the attack, thinking he might end up in Elysium, a paradise for people chosen by the Gods. Thankful to Shun, Charon returns him his pendant and agrees to take him and Seiya to the other side, on the condition they settle the score. Charon explains the contents of the Underworld, consisting of 8 prisons, 3 valleys, 10 pits, and 4 spheres. Seiya and Charon continue their battle. Since Seiya has seen both of Charon's techniques, he is victorious, killing the Specter with his Meteor of Pegasus. Hyoga, Shiryu, Dohko and Kanon have also made it to the Underworld, but are in different parts of it. Seiya and Shun reach the First Prison, the Palace of Justice.

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.

Seiya and Shun reach the Second Prison and encounter Cerberus, the three-headed Watchdog of Hell. Sphinx Pharaoh, guardian of the Second Prison, feeds dead people who were greedy, to Cerberus. The beast tries to eat Seiya, but is defeated by both him and Shun. Suddenly, Lyra Orphée, a legendary Silver Saint just as powerful as the Gold Saints, appears. Pharaoh says that Orphée came to the Underworld willingly and serves Hades. Pharaoh uses Balance of Curse with his harp, about to tear out Seiya's heart. But Orphée plays his lyre and attacks with Stringer Nocturne, defeating the Bronze Saints. He then goes to a garden, visiting his beloved Eurydice, confined to a rock. Seiya and Shun, who survived the attack, arrive in the same garden and encounter Eurydice. She asks them to please help Orphée. She explains that back on Earth, Orphée and Eurydice lived as a couple, in love with each other. However, she was killed when she was bitten by a poisonous snake. Heartbroken, Orphée went to the Underworld, pleading with Hades to revive Eurydice's soul back to Earth, playing his lyre. Pandora lets him know that his request was granted, but on one condition: both must not look back, not even once, until they reached the surface. Wanting to keep Orphée in the Underworld to play his lyre for Hades, Pandora has Pharaoh trick Orphée with a mirror, reflecting a light resembling the sun's light. Orphée turned around, but Eurydice's lower body was confined to a rock. He decided to stay with her since then. Eurydice asks Seiya and Shun to take him back to Earth. Orphée ignores Seiya's request for help to defeat Hades, but Pharaoh appears, taking the Athena Cloth. After learning that Pharaoh reveals he is the reason Eurydice is bound to remain in the Underworld, Orphée prepares to fight Pharaoh.

Orphée plays his lyre, causing Pharaoh to drop the Athena Cloth and allowing Seiya to recover it. Pharaoh plays his harp, and one of Orphée's strings breaks. Pharaoh hates Orphée because he replaced him, entertaining Hades and Pandora with his harp. He then prepares his Balance of Curse, but it backfires. Orphée kills Pharaoh while holding the broken string with his teeth, and uses Stringer Nocturne. Realizing his mistake, Orphée says goodbye to Eurydice and takes Seiya and Shun to a secret passage, leading them to Hades' Palace in the Eighth Prison, Giudecca. Meanwhile, Shiryu, Hyoga and Kanon arrive in the Third Prison, were the dead move giant rocks, equivalent of their greed and desires. They encounter the prison's guardian, Golem Rock, but Shiryu, who is able to see again, easily kills him with a perfect Rising Dragon. Another Specter, Troll Ivan, is also easily killed by Hyoga's Diamond Dust before he gets the chance to properly introduce himself. Orphée arrives in Giudecca, with a trunk (where Seiya and Shun are hidden). Pandora opens it and its filled with flowers, with Orphée wanting to give them to Hades. Not trusting him, Pandora thrusts the flowers with her spear, trying to see if there is anyone in there. Just then, Garuda Aiacos, Wyvern Rhadamanthys and Griffin Minos, the three Judges of the Underworld, arrive in Giudecca.

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.

With words of encouragement from Marin, Seiya gets up and heads towards Giudecca. He finds Shun back to normal and both go deeper into Hades' Temple. Back on Earth, Jabu, Ichi and Nachi see the eclipse, but are confident Seiya and his friends will return. At the orphanage, Seiya's friend Miho and her students also see the eclipse. Seiya and Shun reach the Wailing Wall, which covers the path to the Elysium Fields. Shaka is there and tries to break through, but it is impossible, for only gods can go through it. Saori and Hades are on the other side of the wall. Shaka deduces that Hades' real body is located in the Elysium Fields. Just then, Athena's Cosmos burns throughout the Underworld. Some Specters reach Cocytos and find Valentine's corpse. Just then, Athena's Cosmos revives Aiolia, Mu and Milo. They quickly kill the Specters and as they head for Giudecca, they realize Ikki is gone. Shaka stops Seiya from wasting his energy, trying to break the wall and remembers that the only thing that can destroy the wall is sunlight. Shaka then expands his Cosmo in order to try to make sunlight. Dohko stops him from trying to sacrifice himself. Aiolia, Mu and Milo arrive as well. Mu shows Shaka that most of the beads from the rosary have changed, meaning most of the Specters have died. When all seems lost, Dohko knows how to bring sunlight to the Underworld. He reminds his fellow Gold Saints that their constellations and Cloths surround the Sun in the Ecliptic and have stored sunlight within them. Dohko then distributes his Libra weapons among the Gold Saints in order to destroy the Wailing Wall. Meanwhile, Marin has brought the mysterious girl with her towards the Sanctuary.

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.

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.

Ikki is about to follow his friends, but Pandora warns him that if he enters the path, he will be destroyed, since his Cloth is not bathed in Athena's blood. The six final Specters follow them. Pandora explains that 13 years ago, she lived a peaceful life in Heinstein Castle, before it became Hades' Castle. She lived with her parents, servants and many pets. One day, she found an old shed, locked for 200 years. Curious, she went inside, and found a box with Athena's seal. She opened it, releasing two deities, Thanatos and Hypnos, gods of Death and Sleep. They tell Pandora that her mother will give birth to Hades' soul and order her to take care of it, giving her the power to control the Specters and promising her eternal life. When Hades' reincarnation arrived, everyone except Pandora died in the castle. That was also the reason she went after Shun long ago. After meeting Ikki and the Saints, she realized what Hades promised was a lie and decides to help him, by giving him a necklace that will let him travel to the Elysium Fields safely. Pandora then mysteriously dies, for betraying Hades, but not before warning Ikki of Thanatos and Hypnos, gods and Hades' most loyal servants. The six Specters appear and they are killed by Ikki. With their deaths, all 108 Specters have died. Ikki places the rosary on Pandora's body, promising to avenge her. With his Phoenix wings, Ikki heads to the Elysium Fields. Nymphs warn Thanatos of a "demon" who entered the fields. The god investigates, meeting Seiya, who tells him Saori died. Hypnos, Thanatos' twin brother, appears, and reveals that Thanatos killed Pandora for helping Ikki. However, Hypnos has not killed Saori. Saori is in an urn, located outside a tower where Hades' body is located. Hypnos put her in a deep sleep, and the urn absorbs the blood of its victim. When the urn turns completely red, Saori will die. Seiya rushes to her rescue and Thanatos tries to stop him, but Seiya dodges the attack and counters while running towards Saori. Thanatos finally hits Seiya, destroying his wings. Meanwhile, Shaina, reunited with Marin, Jabu, Ichi, Ban, Geki, Nachi and Kiki, asks Marin where she was. Kiki then brings the mysterious girl from before. Marin reveals the girl's identity: Seiya's long-lost sister, Seika. Seiya hears his sister's voice, and gets up again, attacking Thanatos with his Comet Punch.

Shaina tries talking to Seika, but she has amnesia. She lived all this time in a small village near the Sanctuary. Six years ago, when Seiya came to the Sanctuary, Seika also traveled to Greece, hoping to find her brother, but fell off a cliff, and almost died. An elderly villager found her and rescued her, but she lost her memories since then. Marin knows how Seika felt, because she was also searching for her younger brother. Thanatos recovers from Seiya's attack, but notices blood stains on himself. Angered that he was wounded by a human, he mercilessly attacks Seiya, but then decides to kill Seika from afar as revenge. Shaina and everyone else notice Seika is in pain. Thanatos shows him an manifested image, showing Seiya his sister Seika, telling him he is killing her. Kiki senses a powerful Cosmos about to attack Seika, and he stands in the way of the blast. Kiki senses another blast, and Marin takes the blow this time. Thanatos speaks to them, saying he will kill Seika. A third blast comes, and Shaina takes the hit. Jabu and everyone else burn their Cosmos, surrounding Seika, protecting her, telling Seiya to keep fighting, for they will keep his sister safe. They form a barrier, but Thanatos' blast breaks the barrier, injuring them. Seiya tries using the Pegasus Rolling Crash, but it is useless against the evil god. Shun comes to Seiya's rescue, but Thanatos attacks him as well, destroying the Rolling Defense. Shiryu and Hyoga arrive, but their attacks are useless. Ikki finally arrives. Although he manages to break Thanatos' helmet, Ikki is also no match for Thanatos and suffers his Terrible Providence. However, Thanatos feels a strong vibration, coming from the 12 Gold Cloths. The five Bronze Saints get up again, but the Terrible Providence destroys all five of the Bronze Cloths. Suddenly, five Gold Cloths travel through the dimensions, arriving at the Elysium Fields. Now, Sagittarius Seiya, Libra Shiryu, Aquarius Hyoga, Virgo Shun and Leo Ikki prepare to fight Thanatos.

Aiolos, Dohko, Camus, Shaka and Aiolia's spirits sent their Cloths to help the Saints. Thanatos deduces that Poseidon sent the Cloths to the Elysium Fields. Back on Earth, Sorrento, who is travelling with Julian Solo, senses Poseidon in Julian's body. He tells Sorrento that he has sent the Gold Cloths, though still sealed, in order to help the Bronze Saints and also deduces the Grand Eclipse is launched by Hades, attempting to rule the Earth. Julian comes back to his senses and Poseidon returns to his eternal sleep. Seiya and his friends launch their signature moves against Thanatos at the same time, but they are ineffective, as the evil god destroys the Gold Cloths. Seiya begins to lose hope, but Saori speaks to him, urging him not to give up, since they are still alive. Marin, Shaina, Jabu and the others give him words of encouragement, and as Seiya yells out her name, Seika recovers her memory, screaming out her brother's name. Seiya recovers, burning his Cosmos, and amazingly, his Cloth transforms and covers him, revealing a new Pegasus Cloth. Hypnos appears, revealing it is a God Cloth, an armor capable of rivaling the armors worn by the Olympian Gods. Seiya recovers Athena's Cloth, taken by Thanatos, but as he attacks, Seiya blocks the technique and counters with Meteor of Pegasus, destroying Thanatos' Cloth. Thanatos attacks again, but is finally killed by the Pegasus Comet Punch. Seiya heads for Hades' Tower to save Saori.

Hypnos stands in Seiya's way, but is unable to stop him and Seiya continues towards the tower. Ikki fights Hypnos but is tossed aside. Shun stops Hypnos with his Nebula Chain, as it changes into the Andromeda God Cloth covering his body. Ikki takes the chance to go and help Seiya. Hypnos uses Eternal Drowsiness to lull Shun into a deep sleep. Before Hypnos can kill Shun, Hyoga and Shiryu also awaken their Cygnus and Dragon God Cloth. Seiya finally arrives at Hades' Temple and finds Saori, with the urn almost completely red. Seiya tries attacking the urn, but Hades' soul appears, telling him to give up and that his attacks will come back to him if he launches them. Hypnos tries to make Hyoga and Shiryu fall asleep, but they avoid it, and team up to destroy the God of Sleep, allowing Shun to wake up. Ikki arrives to help Seiya, but after he is attacked, he is exposed to Athena's blood, which awakens the Phoenix God Cloth. Both Saints attack the urn, but are unable to break it. Ikki notices Hades' soul surrounding the Tower, deducing that Hades' body is located there. As Hypnos dies, he warns the Saints to stop Hades from entering his body, otherwise the world will come to ruin. Before Seiya and Ikki reach the body, it's too late. Hades' soul enters his own body, and the God of the Underworld resurrects, setting his sights on Athena, trapped in the urn. After easily repelling Seiya and Ikki's charge, Hades then unsheathes his sword.

Hades tries to slash Athena, but Ikki gets in the way, getting injured in the process. Believing humans will ruin the Earth further, Hades swears to destroy humanity. Shiryu, Hyoga and Shun arrive and all five Bronze Saints combine their signature moves, but it's useless as they are pushed back, yet Hades is injured. Hades is shocked because Seiya resembles another Pegasus Saint that injured him during the previous Holy War. Hades attacks and shows the Saints the Grand Eclipse is near completion. Everyone thinks hope is all lost, but Seika senses that her brother and his friends won't lose so easily. Suddenly, Seiya and the Bronze Saints are protected by energy spheres, made by Saori, allowing them to return to Earth. Saori awakens, recovering her blood. Seiya hands Athena her Cloth, and once she dons it, she breaks the urn and prepares for the final battle against Hades. Both gods question each other's opinions on humanity, with Saori siding with the humans. Hades moves in for the kill, but Seiya launches his Meteor of Pegasus, injuring Hades further. However, Hades' sword pierces Seiya's chest, rendering him out cold, and his Cosmo is disappearing. Saori, Shiryu and the others mourn their friend's defeat, but Saori questions Hades if he knows what love is, saying how strong it can be. Shiryu and the others come back, burning their Cosmos uniting it with Athena's. Saori's scepter pierces Hades' body, killing him. As Hades' Temple and the Elysium Fields crumble, the Grand Eclipse has been extinguished, with the sun shining again upon the world and its inhabitants. Miho, Shunrei, Julian and Sorrento look up at the sky with joy. Jabu, Ban, Ichi, Nachi, Geki, Marin, Shaina, Kiki and Seika are anxious to see Seiya again. Shiryu, Hyoga, Shun and Ikki carry Seiya's body and return with Saori to a world filled with light, as the Holy War between Athena and Hades has ended, forever.