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. Now Hades' Specters, they attack, but Mu is able to block and reflect their techniques with his Crystal Wall. The figure destroys the Crystal Wall and has Deathmask and Aphrodite go and kill Athena. Mu blocks their path and is struck by Deathmask. Suddenly, Seiya comes to Mu's rescue, but is shocked to see the dead Gold Saints alive again. Mu explains that Hades is Athena's true enemy and wants to destroy her to rule the Earth. The true reason the Gold Saints revived in this era, is in order to defeat Hades and his army. Mu also tells him that under Saori's orders, Seiya and his friends are no longer welcome in the Sanctuary, and are to be killed if they disobey. In disbelief, Seiya wears his Pegasus Cloth, even though its damaged, and battles Deathmask, easily overpowering him. However, Mu strikes Seiya from the back, and as Deathmask moves in for the kill, Mu tosses him aside and seemingly destroys Seiya with his Starlight Extinction.

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. The figures reveal themselves as the former Silver Saints Perseus Argol, Auriga Capella, and Cerberus Dante, who were revived thanks to Hades' power. After receiving the Silver Saints' attacks, Shiryu easily kills them with his Rising Dragon. The figures surrounding Mu reveal themselves as the Gold Saints Capricorn Shura, Aquarius Camus, and Gemini Saga, also revived by Hades and after Athena's head. Even though he received Camus and Shura's attacks, Mu stands strong. But all three Specters attack Mu at once. However, he is able to sense that their souls are crying tears of blood. The first figure immobilizes Mu so Saga, Shura and Camus can go through the House of Aries to get Athena's head. Shunrei was unable to stop Shiryu and he heads for the Sanctuary. Roshi arrives and ignites the flames on the fire clock. He has the figure reveal himself, the previous Pope killed by Saga and Mu's master, Aries Shion. Roshi, whose real name is Dohko, is surprised to see his friend and fellow survivor of the previous Holy War, with his 18-year-old body, when he is supposed to be 261 years old, like him. Roshi frees Mu from Shion's telekinesis and tells him to join Aiolia and the other Gold Saints to save Athena while he fights his old friend.

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.