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.

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.

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.

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.