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.

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.

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.

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.