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.

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.

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.

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.