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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 is worried over the disappearance of Athena and frustrated for his failure to protect her and his mentor Shaina. Kōga is determined to master his Cosmo to rescue his goddess. Kōga departs to improve his mastery over Cosmo, later meeting Sōma, the Lionet Bronze Saint, who teaches him about the elements of Cosmo. Eventually, Kōga and Sōma are greeted by the challenge of Mantis Ordykia, one of Mars' henchmen, who puts their command over Cosmo to the test, an experience that strengthens their newfound friendship.

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.

Ryūhō, the son of the legendary Bronze Saint Dragon Shiryū returns to the Palaestra after a short absence. The young Saint apprentices are subjected to a strict training to master their Cosmo element. Kōga is later forced to battle Ryūhō in an intense element-to-element duel.

The young Bronze Saints are taken by Bear Geki to the Hell Camp, which is full of lethal traps composed of the elements of Cosmo. Those who survive the Camp are elligible to become Silver Saints. Kōga and Sōma must work together to overcome the obstacles, all while Sōma must avoid fellow Saint Argo's hostility and haunting memories of his past.

The Saint Fights tournament begins to much anticipation. The young Bronze Saints engage each other in fierce battles, putting their abilities to the test. Kōga manages to attain his first victory after a tense battle, thanks to Sōma's advice; all while his fellow Saints remain intrigued about the seemingly enormous power of Orion Eden.

The Saint Fights tournament continues. Geki and Kōga bond more while the former teaches the young Saint about the mysteries of Cosmo, and reminisces about his defeat at the hands of Seiya years ago. In the tournament, Yuna triumphs over Delphinus Güney, and Kōga and Sōma are pitted against each other in battle. As both are driven by strong motivations, Kōga draws more strength from the memories of Geki to narrowly achieve victory over his friend.

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