Athena Saori watches over peace on Earth from Sanctuary and over young Kōga, until an invader causes commotion when he tries to kidnap Athena and the baby. Kōga is saved from certain death by the timely arrival of Gold Saint Seiya, who engages the mysterious invader, who reveals his identity as Mars. A new conflict begins as Seiya and Mars battle for the fate of Kōga, who years later, determined to live his life as he sees fit, challenges Athena.

Kōga arrives to the Palaestra, guided by Bear Geki and his disciple Sōma. There he is greeted by Saint apprentices, who first approach him with hostility. Also, Kōga meets Aquila Yuna, the young female Saint, who teaches him about his constellation and about the code that guides Saint women.

After his victory over Sōma, Kōga senses a familiar Cosmo approaching, which he recognizes as Athena's. Rushing to meet her, to his surprise, he finds not Athena, but a frail, fearful young girl, whom Capricorn Ionia reveals to be Athena's true self. Ionia also reveals his true allegiance, to Mars, and reveals their plans to a shocked Kōga. After defeating the young Saint, Ionia leaves with the young girl, not before laying waste to the Palaestra, leaving it in ruins. Hours later, Kōga awakens in Mars' Saint Prison, to be greeted by the mysterious Wolf Haruto.

The malevolent entity known as Mars invades Sanctuary, accompanied by Capricorn Ionia and the young girl they claim to be the new Athena. Mars then completely obliterates the millenia-old Sanctuary, replacing it with his very own fortress. Meanwhile, Kōga manages to escape the Saint Prison with the help of Wolf Haruto, and after rejoining the other Bronze Saints, they set off together to invade Mars' headquarters, to rescue the young girl and to learn about the whereabouts of the true Athena

Kōga and his friends continue their trek escorting Aria, until they come to a enormous whirlwind blocking their way. Meanwhile, Mars reveals his plans for his Tower that he deems the new Twelve Zodiac Temples, to his daughter and son, Sonia and Eden. A moribund Athena is also revealed by Mars, held hostage inside his tower. The young Saints decide to brave the whirlwind, managing to find a way inside it with the help of Yuna's command over wind. The traitorous Musca Fly tries to steal Kōga and Yuna's Cloths, only to be defeated in a fierce battle. Weary and alone, the young Saints find a new light of hope in the Pegasus constellation, which reveals a message from the legendary Seiya: "To you, I entrust Athena!"

Learning of Souma's defeat, Eden leaves the Sanctuary in order to find Aria himself. He eventually manages to track down Aria, who is accompanied by Kouga and Yuna. After easily defeating Yuna, Eden and Kouga have their long awaited fight. However, the Orion Bronze Saint easily dominates the battle despite Kouga's best efforts. Not wanting to see her friend hurt, Aria allows Eden to take her away.

Knowing of Aria's whereabouts, the Bronze Saints set off to invade the final ruins, followed by Ophiuchus Shaina, who joins them. Before parting, Shaina reveals to Kōga the secret of his origin, as well as Aria's. Inside the ruins, the Bronze Saints face the threat of powerful Silver Saints, while Kōga engages Orion Eden to free Aria. Shaina takes Aria and with her help, they are able to vanquish Mars' dominion over the area. As Mars' power vanishes, the ruins crumble, and the bronze Saints realize Mars' dark power is emerging from the debris of the structure.

Eden sees his own darkness as Aria is constantly being used by Mars without the power to do anything about it, before being confronted by his parents about his destiny for the new world. Accepting whatever punishment that would be suitable for his errors, Eden allows himself to succumb to his darkness. Meanwhile, tormented by her own darkness of being used as an instrument of destruction Aria resolves to use her Light to protect those who need her, in doing so she reaches both Eden and Kouga from their darkness and all reach the Core of Darkness. Aria then along Kouga...

Eden takes over the fight against Fudo after blasting Kouga and the others out of the Virgo Temple. Following a desperate battle, Eden manages to defeat the Virgo Gold Saint when he awakens the seventh sense. At the same time, the other Bronze Saints attempt to use the opening he gave them to go to the Libra Temple. Unfortunately, they are confronted by Tokisada, the new Aquarias Gold Saint and the man who killed Haruto's brother. His apparent ability to control time makes him a powerful adversary and Kouga is defeated with little effort.

Kouga and Yuna reach the House of Capricorn where they meet Ionia and learn from him his reasons for betraying Athena. Kouga attacks the former Headmaster of the Palaestra, but is once again immobilized by his Domination Language technique, and his Darkness Cosmo is brought out. Before Yuna is able to help Kouga keep the Darkness Cosmo at bay, Ionia buries her in a rubble of books, facing Kouga alone. However, after succeeding to repress the Darkness Cosmo in his heart, Kouga awakens his Seventh Sense and finally kills Ionia with the legendary Pegasus Comet Punch.

Sending Kouga ahead Eden awakens his Seventh Sense and challenges Mars, immobilizing him with his Cosmo. Eventually, while Kouga struggles to retrieve Aria's staff at the top of the Sanctuary, Mars breaks free and grievously wounds Eden, temporarily defeating him. Pursuing Kouga, Mars easily shrug off any attack from the Pegasus Saint until Eden finally catches up to the two. Bringing their Cosmos to the limit, Kouga and Eden finally defeat Mars together and have Ludwig return to his senses. However, just as Ludwig is about to retrieve Aria's staff to prevent Earth's ...

Yuna, the only one left standing after Abzu's terrifying onslaught against Kouga's friends, is encouraged by Athena to fight against Abzu in order to bring Kouga back. However, all her attempts fails, gaining her darkness wounds for each attempt. Just then, the fragments of Aria's staff combined with Kouga's friend's Cosmos awaken Seiya, who has been trapped in the depths of the red planet all this time, waiting for a chance to stop Abzu's plans. The Gold Saint confronts Abzu and manages to drive him from Kouga's body with aid from Yuna. The God of Darkness then flees...

Abzu tries to have Kouga under his control once more with no success and his attempts to kill Saori are stopped by his desperate efforts. Once feeling the radiance of his Cosmo, Kouga's friends send the last of their energies to assist him. Infused with the power of his companions and protected by Aria's light, Kouga manages to rescue Saori and destroy Abzu for good. As Earth regains the Cosmo that was siphoned from it, the planet returns to normal and the corruption that has spread into the Saints' bodies is washed away. After a brief encounter with Aria's spirit, ...