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.

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.

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.

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 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.

Souma and Sonia are entrapped in an illusion of their past when Souma's father Southern Cross Kazuma was alive. Sonia is revealed to have been ordered by Medea to kill the Silver Saint for he was an open leader against the Martians. Hesitant on her mission she departs and faces Kazuma, as Souma also witnesses the past event. Sonia is first easily pushed away by Kazuma who tells her that her fists are made to protect those she care for, but when she thinks of her family, Sonia bursts into a rage and stabs Kazuma from the back. It is revealed then that after the murder,...

After the defeat of Kouga at the hands of Harbinger, the remaining Bronze Saints engage him in battle, meeting with utter defeat. Harbinger reminisces about his difficult childhood and what drove him to a life of violence, to become the strongest and eventually a Gold Saint. Managing to recover after witnessing the defeat of his comrades, Kouga attacks Harbinger with a single blow imbued with all the power of his Cosmo. Much to his surprise, Harbinger emerges unscathed and his comrades have vanished.

Because of Schiller's Praesepe Underworld Waves, Yuna leaves the earthly plane and finds herself in the deathly Hill to the Land of Spirits. Terrified by the sight of the souls of the deceased and visions of her sordid past, Yuna cowers until the arrival of Kouga, who suffered her same fate, and losing his temper due to Schiller's mockery of Aria's death, Kouga is consumed by the Darkness Cosmo inside him. Managing to calm down Kouga, Yuna engages the Cancer Gold Saint in battle once again, and drawing from her bonds to Aria and her comrades, she finally finds the ...

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 ...

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...

Unaware of the advent of the Pallasites, Ryuhou believes that there is no reason to fight anymore and wants to return the Dragon Cloth to his father Shiryu, whose senses were restored, and live peacefully with his family. Meanwhile, Koga and the others learn that a Pallasite is after Ryuhou and rush to assist him, but when Ryuhou finds himself struggling to protect his mother Shunrei from the enemy, his renewed determination awakens his true power as the Dragon Saint and the new Dragon Cloth.

Koga and Subaru are sent by Shina to investigate the disappearance of a Silver Saint. Upon finding their missing companion, they are approached by the Secondary Pallasite Europa and the Tertiary Pallasite Thebe and learn, much to their surprise that Eden is now working with them as a Tertiary Pallasite, with the promise of having Aria and the rest of his family revived. With orders to kill Koga, Eden attacks him mercilessly until Thebe decides to intervene and the Orion Saint reveals his true intentions as well as his new Orion Cloth.

Ryuhou, Souma, and Yuna arrive to a village whose survivors of the Pallasite Halimede's attack are under Shun's protection. Among them is Ray, a child whose brother was also frozen by Halimede and blames Shun for it. Halimede instructs Ray to steal the Andromeda Cloth Stone from Shun with the promise of having his brother return to normal, but when the enemy intends to kill both, Shun brings the power of his cloth to the next level.

Now knowing where Pallas is located, Seiya decides to lead an attack on her stronghold with the intention to kill her. On the way to meet him there, Koga and his friends are ambushed by the Tertiary Pallasite Cyllene and Haruto stays behind to confront him. Subaru decides to assist him ignoring his friends' warning and the two find later that they must fight not only Cyllene but also his twin brother Greip.

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.

The second day of battles begin, and Koga, Ryuhou, Haruto, and Subaru take a chance to make a beeline for the Palace until they are intercepted by Mira, a Pallasite of unknown rank who fights without donning his Chronotector. Despite seemingly at a disadvantage, Mira easily overpowers the party with his speed and his Alchemy Glove's mysterious power to destroy Saint Cloths just by touching them, until Haruto realizes his trick and comes up with a way to fight back, but Mira is barely scathed by the counter. Just as he is about to don his Chronotector, he is ...

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.

At last Koga arrives at the front of Pallas' castle, which is sealed by the "Gate of Time", a massive door reinforced with Titan's powers. Koga attempts to break through the gate by himself but his own life is put in danger instead, until Athena and her Saints arrive to lend a hand.

Tokisada, the former Aquarius Gold Saint who was supposed to be defeated by Haruto at the End of Time, appears before him as a Secondary Pallasite at the second path, donning a Chronotector that enhances his time-control abilities. Haruto, Eden and Subaru have a hard time against him until Hyoga appears to battle him in their place.

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.

The young Bronze Saints face off against Gallia on their own, allowing the Gold Saints and Athena to move forward towards Pallas. Although Gallia's Photontector and Bushin Photon Sword seem impervious to harm, Subaru once more calls on the mysterious powerful cosmo to break through Gallia's offensive and actually damage the sword, convincing the others to call upon their own cosmo, transforming their New Cloths into the more powerful Omega Cloths, and together the six Bronze Saints defeat Gallia.

Accompained only by Seiya and Harbinger, Saori finally comes face to face with Pallas. Titan steps in to protect his master and Harbinger challenges the Pallasite, using Athena's cloth to draw his attention. Treating him as a mere ruffian, Titan is surprised by the true might of the Taurus Saint, who proves himself far more powerful and noble than he claims to be.

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.