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.

Ikki is about to follow his friends, but Pandora warns him that if he enters the path, he will be destroyed, since his Cloth is not bathed in Athena's blood. The six final Specters follow them. Pandora explains that 13 years ago, she lived a peaceful life in Heinstein Castle, before it became Hades' Castle. She lived with her parents, servants and many pets. One day, she found an old shed, locked for 200 years. Curious, she went inside, and found a box with Athena's seal. She opened it, releasing two deities, Thanatos and Hypnos, gods of Death and Sleep. They tell Pandora that her mother will give birth to Hades' soul and order her to take care of it, giving her the power to control the Specters and promising her eternal life. When Hades' reincarnation arrived, everyone except Pandora died in the castle. That was also the reason she went after Shun long ago. After meeting Ikki and the Saints, she realized what Hades promised was a lie and decides to help him, by giving him a necklace that will let him travel to the Elysium Fields safely. Pandora then mysteriously dies, for betraying Hades, but not before warning Ikki of Thanatos and Hypnos, gods and Hades' most loyal servants. The six Specters appear and they are killed by Ikki. With their deaths, all 108 Specters have died. Ikki places the rosary on Pandora's body, promising to avenge her. With his Phoenix wings, Ikki heads to the Elysium Fields. Nymphs warn Thanatos of a "demon" who entered the fields. The god investigates, meeting Seiya, who tells him Saori died. Hypnos, Thanatos' twin brother, appears, and reveals that Thanatos killed Pandora for helping Ikki. However, Hypnos has not killed Saori. Saori is in an urn, located outside a tower where Hades' body is located. Hypnos put her in a deep sleep, and the urn absorbs the blood of its victim. When the urn turns completely red, Saori will die. Seiya rushes to her rescue and Thanatos tries to stop him, but Seiya dodges the attack and counters while running towards Saori. Thanatos finally hits Seiya, destroying his wings. Meanwhile, Shaina, reunited with Marin, Jabu, Ichi, Ban, Geki, Nachi and Kiki, asks Marin where she was. Kiki then brings the mysterious girl from before. Marin reveals the girl's identity: Seiya's long-lost sister, Seika. Seiya hears his sister's voice, and gets up again, attacking Thanatos with his Comet Punch.

Shaina tries talking to Seika, but she has amnesia. She lived all this time in a small village near the Sanctuary. Six years ago, when Seiya came to the Sanctuary, Seika also traveled to Greece, hoping to find her brother, but fell off a cliff, and almost died. An elderly villager found her and rescued her, but she lost her memories since then. Marin knows how Seika felt, because she was also searching for her younger brother. Thanatos recovers from Seiya's attack, but notices blood stains on himself. Angered that he was wounded by a human, he mercilessly attacks Seiya, but then decides to kill Seika from afar as revenge. Shaina and everyone else notice Seika is in pain. Thanatos shows him an manifested image, showing Seiya his sister Seika, telling him he is killing her. Kiki senses a powerful Cosmos about to attack Seika, and he stands in the way of the blast. Kiki senses another blast, and Marin takes the blow this time. Thanatos speaks to them, saying he will kill Seika. A third blast comes, and Shaina takes the hit. Jabu and everyone else burn their Cosmos, surrounding Seika, protecting her, telling Seiya to keep fighting, for they will keep his sister safe. They form a barrier, but Thanatos' blast breaks the barrier, injuring them. Seiya tries using the Pegasus Rolling Crash, but it is useless against the evil god. Shun comes to Seiya's rescue, but Thanatos attacks him as well, destroying the Rolling Defense. Shiryu and Hyoga arrive, but their attacks are useless. Ikki finally arrives. Although he manages to break Thanatos' helmet, Ikki is also no match for Thanatos and suffers his Terrible Providence. However, Thanatos feels a strong vibration, coming from the 12 Gold Cloths. The five Bronze Saints get up again, but the Terrible Providence destroys all five of the Bronze Cloths. Suddenly, five Gold Cloths travel through the dimensions, arriving at the Elysium Fields. Now, Sagittarius Seiya, Libra Shiryu, Aquarius Hyoga, Virgo Shun and Leo Ikki prepare to fight Thanatos.

Aiolos, Dohko, Camus, Shaka and Aiolia's spirits sent their Cloths to help the Saints. Thanatos deduces that Poseidon sent the Cloths to the Elysium Fields. Back on Earth, Sorrento, who is travelling with Julian Solo, senses Poseidon in Julian's body. He tells Sorrento that he has sent the Gold Cloths, though still sealed, in order to help the Bronze Saints and also deduces the Grand Eclipse is launched by Hades, attempting to rule the Earth. Julian comes back to his senses and Poseidon returns to his eternal sleep. Seiya and his friends launch their signature moves against Thanatos at the same time, but they are ineffective, as the evil god destroys the Gold Cloths. Seiya begins to lose hope, but Saori speaks to him, urging him not to give up, since they are still alive. Marin, Shaina, Jabu and the others give him words of encouragement, and as Seiya yells out her name, Seika recovers her memory, screaming out her brother's name. Seiya recovers, burning his Cosmos, and amazingly, his Cloth transforms and covers him, revealing a new Pegasus Cloth. Hypnos appears, revealing it is a God Cloth, an armor capable of rivaling the armors worn by the Olympian Gods. Seiya recovers Athena's Cloth, taken by Thanatos, but as he attacks, Seiya blocks the technique and counters with Meteor of Pegasus, destroying Thanatos' Cloth. Thanatos attacks again, but is finally killed by the Pegasus Comet Punch. Seiya heads for Hades' Tower to save Saori.

Hypnos stands in Seiya's way, but is unable to stop him and Seiya continues towards the tower. Ikki fights Hypnos but is tossed aside. Shun stops Hypnos with his Nebula Chain, as it changes into the Andromeda God Cloth covering his body. Ikki takes the chance to go and help Seiya. Hypnos uses Eternal Drowsiness to lull Shun into a deep sleep. Before Hypnos can kill Shun, Hyoga and Shiryu also awaken their Cygnus and Dragon God Cloth. Seiya finally arrives at Hades' Temple and finds Saori, with the urn almost completely red. Seiya tries attacking the urn, but Hades' soul appears, telling him to give up and that his attacks will come back to him if he launches them. Hypnos tries to make Hyoga and Shiryu fall asleep, but they avoid it, and team up to destroy the God of Sleep, allowing Shun to wake up. Ikki arrives to help Seiya, but after he is attacked, he is exposed to Athena's blood, which awakens the Phoenix God Cloth. Both Saints attack the urn, but are unable to break it. Ikki notices Hades' soul surrounding the Tower, deducing that Hades' body is located there. As Hypnos dies, he warns the Saints to stop Hades from entering his body, otherwise the world will come to ruin. Before Seiya and Ikki reach the body, it's too late. Hades' soul enters his own body, and the God of the Underworld resurrects, setting his sights on Athena, trapped in the urn. After easily repelling Seiya and Ikki's charge, Hades then unsheathes his sword.

Hades tries to slash Athena, but Ikki gets in the way, getting injured in the process. Believing humans will ruin the Earth further, Hades swears to destroy humanity. Shiryu, Hyoga and Shun arrive and all five Bronze Saints combine their signature moves, but it's useless as they are pushed back, yet Hades is injured. Hades is shocked because Seiya resembles another Pegasus Saint that injured him during the previous Holy War. Hades attacks and shows the Saints the Grand Eclipse is near completion. Everyone thinks hope is all lost, but Seika senses that her brother and his friends won't lose so easily. Suddenly, Seiya and the Bronze Saints are protected by energy spheres, made by Saori, allowing them to return to Earth. Saori awakens, recovering her blood. Seiya hands Athena her Cloth, and once she dons it, she breaks the urn and prepares for the final battle against Hades. Both gods question each other's opinions on humanity, with Saori siding with the humans. Hades moves in for the kill, but Seiya launches his Meteor of Pegasus, injuring Hades further. However, Hades' sword pierces Seiya's chest, rendering him out cold, and his Cosmo is disappearing. Saori, Shiryu and the others mourn their friend's defeat, but Saori questions Hades if he knows what love is, saying how strong it can be. Shiryu and the others come back, burning their Cosmos uniting it with Athena's. Saori's scepter pierces Hades' body, killing him. As Hades' Temple and the Elysium Fields crumble, the Grand Eclipse has been extinguished, with the sun shining again upon the world and its inhabitants. Miho, Shunrei, Julian and Sorrento look up at the sky with joy. Jabu, Ban, Ichi, Nachi, Geki, Marin, Shaina, Kiki and Seika are anxious to see Seiya again. Shiryu, Hyoga, Shun and Ikki carry Seiya's body and return with Saori to a world filled with light, as the Holy War between Athena and Hades has ended, forever.