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.

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.

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.

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.

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.