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.

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.

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.