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 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.

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.

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.

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.

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.

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, ...

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 arrives at the House of Scorpio, watching Souma right next to Sonia's body. Souma apologizes to Eden before moving to catch up with Kouga and Yuna. Meanwhile, Haruto and Ryuuhou awaken at the End of Time, finding themselves confronted by Tokisada, whose time-manipulating powers have regained their strength after his fight against Genbu. From the moment the battle begins, Tokisada easily gains the upper hand against the two Bronze Saints' combined strength. At the same time, Kouga and Yuna reach the House of Sagittarius, supposed to be protected by Seiya. Upon ...

Kouga defeats one of the Heavenly Kings in one hit before he manages to once again keep his Darkness Cosmo due to him having reached his Seventh Sense earlier and Yuna calling out to him. Sending him ahead, Yuna engages Amor while Souma, Ryuuhou and Haruto engage the remaining three Heavenly Kings, using the last bit of strength they have left in order to finally defeat them. Leaving the rest to Kouga, they collapse to exhaustion. Amor decides to fight Yuna, but is interrupted by Eden who has arrived as well. Following a short fight, Yuna asks Eden to go onward and ...

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 ...

With Yuna, Souma, and Ryuhou leaving ahead to the Sanctuary, Koga and Subaru look for Haruto in Japan and find, much to their surprise, that he is now a singer in a rock band. Haruto rejects Koga's pleas to return, claiming that to him, his music is now more important than being a Saint. However, during a concert, Haruto watches Koga and Subaru being attacked by some Pallasites, and to protect his friends and his fans, he dons his brand new Wolf Cloth to join the battle.

Aegir fails to defeat Genbu by himself and the Primary Pallasite Hyperion lends his own sword to assist him. Overwhelmed by the massive Cosmo flowing from the sword, the Gold Saint decides to forfeit his own life in an attempt to destroy it.

Eden wanders through the city drawn by a strange cosmo when he meets the Secondary Pallasite Europa and is saved by Seiya. Inspired by the Gold Saint to look for a reason to fight, Eden pursues Europa who was sent in a mission to kill Koga, but has a hard time fighting the enemy until Subaru unleashes an impressive power that was dormant within him.

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.

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.

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.

Fudo, Kiki, and Shiryu face off against Hyperion, allowing Athena, Seiya, and Harbinger to move forward. Hyperion's Destruction Tector and Tenchi Destruction Slash holy sword prove too powerful for the three Gold Saints' attacks on their own. In a final show of strength, they combine their Cosmo into a single forbidden attack: Athena Exclamation. The Saints and Pallasites throughout Pallasvelda react to the outpouring of Cosmo, and as the Tenchi Destruction Slash is destroyed, the three Saints' Cosmo vanishes.

As Subaru's time is taken away by the Chrono Destruction, Koga, Yuna, Souma, Ryuhou, Haruto, and Eden still have to face the immense power of Hyperion as well as awaken their greater Omega Cosmo.

Sagittarius Seiya faces off against Saturn, the God of Time, and Shun and Hyoga protect Athena and Pallas from Europa and Mira.