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.

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.

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 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.

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 arrives at the House of Cancer, and she is greeted by the deathly atmosphere of the gates of Praesepe. The guardian of the House, Cancer Schiller, engages her in battle, reminiscing about his past and motives for his allegiance to Mars. Aiming for Yuna's utter defeat, Schiller tries to break her morale by toying with her psyche, having Yuna fight her deceased friends Arné and Komachi. Meanwhile, Kouga continues his battle with Harbinger. After another clash between the two Saints' greatest techniques, Kouga heads towards the exit. Admiring his determination, ...

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.

The Bronze Saints finally arrive to the House of Pisces, guarded by the ruthless Amor. After separating Kouga and Yuna from the others, Amor summons Mars' strongest warriors, the Four Heavenly Kings to fight the others. While stating that the Heavenly Kings are stronger than the Gold Saints, Amor immobilize Yuna, forcing her to watch her friends being attacked without resisting. Kouga, the only one capable of attacking, is restrained by Amor's Arrested Judgement, a special attack that can only be broken by Darkness Cosmo as part of Medea's plan to have him unleash the...

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 ...

Eden tries to stop Abzu with no success until he gets the chance to obtain Aria's staff to confront him. Medea tries to dissuade him, but he refuses to comply and reclaims the staff by force. With Kouga's friends failing to get him back to normal despite everyone awakening their Seventh Sense, Eden eventually returns with the staff to the battle, just to find it destroyed by Abzu. Just as Eden is about to be dealt the final blow by the God of Darkness, Medea stands to protect her son, sacrificing herself for him. However, Eden is still dealt a heavy attack while the ...

Koga and Subaru return to the Palaestra which is full of refugees from the villages attacked by the Pallasites and rendezvous with their friends. Genbu approaches the Bronze Saints and, noticing how much their cloths are damaged, reprimands them for relying too much on them instead of their own abilities. When a large enemy force led by the secondary Pallasite Aegir surrounds the Palaestra, Genbu decides to face it head on by himself, while taking the opportunity to share with Koga and the others what he has learned from his teacher, the previous Libra Saint.

As the battle intensifies, Souma and Subaru fall back to assist the other Steel Saints in time to rescue only two of them, Kerry and Emma. Soon after, they are attacked by Loge and forced to retreat once Souma is injured. Surrounded by the enemy forces, Souma and the Steel Saints must work together to break Loge's siege and fight back.

On their way to the palace, Koga and his friends meet Celeris, who fights to protect the refugees with the Equuleus Cloth, despite taking heed of the dreaded curse that befalls whoever dons it. They also meet Selene, a young girl who takes care of all the humans who hide underground who has not been frozen in time, and Eden, with something to protect, has to fight Thebe once again, while Subaru and Celeris encounter Hati and have a short battle with him.

As Saori and her escorts advance through the city overcoming all opposition, Ryuhou is separated from his fellow Bronze Saints by Paradox, who returns as a Secondary Pallasite for a rematch. Paradox's sister Integra appears to assist him as the new Gemini Gold Saint, while the last of the legendary saints, Phoenix Ikki, prepares himself to join the battle as well.

Once inside the castle, Saori and the Saints are informed by Europa that only one of the four separate paths ahead of them lead to Pallas, and flees soon after, thus they decide to split up. Meanwhile, the Heavenly Kings conspire together not only against Athena, but against Pallas as well.

While Eden questions Subaru who he really is, Koga, Souma, Yuna, and Shun encounter the Primary Pallasite Aegaeon who wants to test the Bronze Saints' powers himself. After telling the Saints about how Ikki put his life on the line to crack Aegaeon's sword, Shun has a hard time fighting him until Koga, Souma, and Yuna keep fighting the Pallasite, defending Shun. Burning his Cosmo to the maximum, Koga manages to give Aegaeon a crack to his sword, before Ikki arrives to save the Bronze Saints, taking over the battle.

Athena, Seiya, Kiki, Fudo, and Harbinger are attacked by their former Gemini Gold Saint ally turned Secondary Pallasite Paradox. Integra, the new Gemini Saint and Paradox's twin sister, arrives to protect Athena and settle their score. Once defeated, Paradox is forgiven by Saori and reforms, just to be later fatally wounded by the Primary Pallasite Gallia.

Seiya is defeated by Saturn before Kouga and his friends also fall before his almighty power, following a desperate battle in which the Bronze Saints are defeated one by one. When all seems lost, Athena gathers the Cosmos of all the other Saints to restore Kouga, who rises again as the ultimate Omega Saint, determined to stop the God of Time once and for all.