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

The young Bronze Saints bravely invade Mars' Babel Tower, and succeed in rescuing the girl he claims to be Athena. She reveals to Kōga that her name is Aria. Sensing a threat approaching, Kōga dispatches Yuna along with Aria to avoid being recaptured, and together, the young Saints try desperately to buy time for their escape by facing the seemingly invincible Leo Mycene. In their darkest hour, a memory of Seiya deep in Kōga's heart brings them hope.

Yuna arrives with Aria to a small town. In Babel, Mars send Sonia (the Highest Martian), The Crow and Miguel of the Hound (Silver Saints) after them. Miguel guides the bad gang to the town where Aria and Yuna are in a church. Aria is left hidden and Yuna goes to fight. Right when Sonia is about to kill Yuna, one martian arrives asking Sonia to go back to Babel for a meeting of Mars with all the Saints. It is revealed that she killed Soma's father. She leaves and the Crow is beating Soma and Yuna. Koga save them and help Yuna to deliver a fatal blow on Crow. In Babel: Yuna, Soma, Koga, Ryuho and Haruto are blamed for Santuary destruction and taking Athena apart. So all the Saints are looking for them.

Kōga and friends continue their trek to take Aria to safety, when they're surprised by the attack of Hound Miguel. Overpowered by the merciless Silver Saint, the lives of the Bronze Saints are saved by the timely arrival of Andromeda Shun, the Saint of legend. Shun takes the youngsters to his village to rejoin Ryūhō, afterward they're once again attacked by Miguel, whom they manage to defeat after a fierce battle. Later, the young Saints leave Shun's village to continue their mission.

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!"

The Bronze Saints reach a snow-covered land, which causes Yuna to reminisce about her days as a Saint apprentice and her mentor, the kind Peacock Pavlin. Sensing her mentor near, Yuna rushes to her encounter, only to realize Pavlin's allegiance is to Mars. Disciple and master engage in a fierce duel, later Yuna realizes it was Pavlin testing her, as her mentor reveals she is truly loyal to Athena Saori, and informs Yuna she is still alive and being held hostage by Mars. As Yuna prepares to rejoin her fellow Bronze Saints, both female Saints are surrounded by traitorous Silver Saints. Pavlin stays behind to cover Yuna's escape, seemingly losing her life.

The episode begins with our heroes walking through the woods as we find they are looking for the Earth Cosmo Core. Haruto appears, informing them that there is a town in front of them and a visitor behind them before he disappears once more, despite them asking him to stay. The "visitor" turns out to be Ichi, the older Saint from Palestra that was never able to use his powers correctly, and since that time the bronze saints found some surprises along the way.

Resuming their journey, the Bronze Saints eventually are tracked down by a small cadre of Martians. Running away from them to protect Aria, the teenagers reach a small but lively city, where Yuna fails to purchase a ship ticket as her purse fell during their escape. In order to rise money for ship fare, the Saints eventually find a job thanks to a kind old man who takes them to his wife's restaurant, where the youngsters prove they are not up to the challenge, much to the woman's chagrin. Later, the Martians are able to find the Saints and a fierce battle ensues. After achieving victory, the young Saints receive a resounding ovation from the crowd, and are given another chance at the restaurant.

The Bronze Saints arrive to a desert area, in which they meet a young girl from the people of Jamir, called Raki, who at first attacks them. After realizing they are Saints, by tradition connected to the people of Jamir, Raki takes them through a shortcut to avoid the desert areas, only to be greeted by the challenge of Kerberos Dorie, who seeks to capture Aria. Managing to defeat Dorie after a difficult battle, the Bronze Saints resume their journey, bidding farewell to their young benefactor, who later is joined by her mentor, Appendix Kiki, the former apprentice of the legendary Aries Mu, now a young man, who realizes the Bronze Saints are the new embodiment of hope in this era.

The Bronze Saints reach the Fire Ruins where Sonia finally comes across the murderer of his father, Hornet Sonia. Souma engages in a giant battle with her but his anger continues to lose his own focus and is unable to hit her. The battle proves fruitless until Koga manages to convince him to control his emotions. This allows Souma to finally hurt Sonia for real and she escapes beaten. After stopping the ruins, Souma realizes that he cannot stay with the team until he has settled things with Sonia and departs on his own.

After Sōma's fateful battle, the Bronze Saints reach the famed Lushan fairylands in China, and are rejoined by Dragon Ryūhō. Shortly afterward, the teens suffer the assault of the ferocious Perseus Mirfak, who turns them to stone, with the exception of Ryūhō, who barely manages to defeat Mirfak, repeating the miraculous feat his father performed years ago, against Perseus Algol. Continuing their journey, the Saints tresspass the Lushan waterfall with the help of the Libra Gold Cloth, only to be greeted by the challenge of a mysterious young man named Genmu, who takes the Libra Gold Cloth as his rightful heirloom, as he reveals himself to be the Libra Gold Saint.

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.

Eden takes Aria away, and Aquila Yuna and Pegasus Kōga resume their journey, demoralized by their failure to protect their friend. Along the way, Yuna and Kōga separate, meanwhile Eden and Aria reminisce about the happy days they shared during their childhood. Kōga later meets a young man who first mocks his weakness, luring the teen Saint into a fight. Kōga later realizes the man to be the owner of an immense Cosmo, and turns out to be Cygnus Hyōga, one of the legendary Saints who protected Earth from great menaces many years ago. Hyōga manages to teach Kōga that to reach the true potential of his Cosmo, he must first believe in himself. After learning Hyōga's lesson, Kōga rejoins Yuna and both resume their way with renewed resolve.

Haruto, accompanied by Ryuhou, journeys to his home village in an attempt to come to terms with his past and regain his resolve. While there, Ryuhou learns that Haruto became a saint in order to follow the footsteps of his good friend and older brother figure Yoshitomi, the previous Wolf Saint. Yoshitomi had apparently been murdered by a masked silver saint in front of Haruto and the boy had been desperate for answers ever since. Haruto's fater, despite his disapproval of Haruto becoming a saint, helps him gain back his fighting spirit by staging an assassination attempt on his son's life.

The young Bronze Saints decide to invade Mars' stronghold to rescue Aria. The teenagers carry out their plan, finding strong opposition in the enemy lines. During a moment of desperate need, the Bronze Saints receive the assistance of Lionet Sōma, who rejoins them, stronger than before, thanks to further training under Unicorn Jabu, the Bronze Saint. The Saints reach Aria's chambers, only to find she has left. Not all is lost, as Sōma is able to retrieve the Southern Cross Cloth's Clothstone, which belonged to his father Kazuma, after defeating Hornet Sonia, his killer.

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.

Yuna, Ryuuhou and Haruto are transported to an unknown dark place and eventually reach a door, which they touch and are all transported to a world of memories. Yuna is on her hometown with her childhood friend before the war, Ryuuhou is on his childhood on Palestra along with his then friend Lynx Mirapolos and Haruto faces his own brother Yoshitomi. All three realize the world they are in is an illusion created by the darkness in their hearts and are at first hesitant to battle, but manage to overcome the darkness and reach the Core of Darkness.