At the orphanage, Patricia's hands are glowing. Shortly after, a group of soldiers arrive to abduct her. Before they can take her away, the Gold Knight Leo Aiolia appears, defeats the soldiers and abducts Patricia, having sensed Cosmo in her. Despite her younger brother Seiya's attempts to save her, she is abducted, leaving him distraught. A few years later, during a scuffle, Seiya discovers that he too possesses Cosmo. After returning to the orphanage to get some rest, Seiya is abducted and finds himself in a room where he is greeted by the enigmatic Alman Kido, who has been watching Seiya, witnessed his Cosmo awakening and now requests Seiya to become the Pegasus Bronze Knight, convinced that this is his destiny.

Seiya arrives at Chamos Island by Alman's request but is confronted by a group of Sanctuary guards. The Silver Knight Eagle Marin prevents the guards from executing Seiya once she hears his name, taking him as her own student. After 6 years of training, Seiya defeats Cassios and finally obtains the Pegasus Armor. Despite the Grand Master's warning that Knights are forbidden to fight for anything else but Athena, Marin instructs Seiya to participate in the Galaxian Wars. Despite not understanding why, Seiya obliges and locates a secret underground base in the desert, where he reunites with Sienna and Mylock, and also meets several other Bronze Knights who have obtained their own Armors.

Andromeda Shaun faces Unicorn Jab, easily dodging his attacks before she retaliates and defeats Jab in one strike. Shortly after, her chains start rattling before the box containing the Gold Armor suddenly opens, revealing that it's right arm bracer is missing. The Bronze Knights then find themselves under attack and, upon exiting the underground base, find themselves confronted by a vast army of Guraad's soldiers. Following a vicious battle where they drive of Guraad's forces, Shaun's chains act up again, pointing at the Gold Armor.

Nero easily incapacitates Seiya, Long, Shaun and Magnus before taking off with the Gold Armor. The Bronze Knights rendezvous with Sienna and Mylock, where Magnus casts aside his earlier suspicions and confirms that Sienna truly is the reincarnation of Athena. Pledging their loyalty to Sienna, the Bronze Knights pursue Nero on his aircraft, knocking it down from the sky. Seiya arrives at the crash site first, where he confronts Nero, who has a group of Black Knights with him, created by Guraad who has managed to use the Sagittarius Gold Armor to create his own army of Knights.

Shaun attempts to talk with Nero and convince him to not give in to hate. But Nero refuses, striking down Shaun before effortlessly neutralizing Long and Magnus' attacks. Meanwhile, at the Five Old Peaks, the Old Master is visited by a man named Mū, who expresses concern over only observing as the Bronze Knights fight among themselves, wanting to take action and help. The Old Master advices him to remain calm and stay his hand for the time being.

Seiya awakens on a beach, being greeted by a kid named Kiki. His master, Mū, saved Seiya and the other Bronze Knights, except Nero, who had instructed Mū to save the others instead of him. Just then, Marin and the Silver Knight Lizard Misty arrive to assassinate Seiya, at the orders of the Grand Master. Seiya equips his Armor and engage Misty in battle, but he is no match for the more experienced warrior. Just as Misty is about to deal the final strike, however, Marin steps between and attacks Seiya instead.

Recovering from Misty's attack, and worried about Sienna's safety, Marin orders Seiya to return to protect her, after revealing that Shaun, Magnus and Long are still alive, the buried corpses being Black Knights. Once he leaves, she attempts to face Asterion and Morris by herself, once they return to check on Misty. The Silver Knights easily overpower her due to Asterion's mind-reading abilities, and they incapacitate her, forcing Seiya to turn back. Returning to the beach, Seiya battles Morris but is easily overpowered.

Seiya is reunited with Long, Magnus and Shaun who is saddened to learn that Nero refused to be saved, before they rendezvous with Sienna by the waterfalls. Discussing the prophecy about Sienna as Athena, Seiya promises to protect her, regardless of whether the prophecy is true or not. Just then, a pair of crows emerge from the forest. The Bronze Knights rush to find Mylock unconscious and the Silver Knight Crow Jamian perching on a cliff. The four engage him but are easily overwhelmed by his army of crows, acting as Jamian's arms and legs. They are then covered in black feathers from the crows, immobilizing them. Seiya manages to break free and pursues Sienna, who has been abducted by the crows.

Shaun, Magnus and Long arrive to help Nero, who takes his leave, preferring to fight alone. As soon as he leaves, Argol uses his Medusa Shield to turn Shaun into stone. Remembering the legend of Perseus and Medusa, Magnus attempts to use his shield to get close but he is easily defeated and turned to stone as well. With Sienna slowly turning into stone as well, and out of options, Long injures his eyes and finally kills Argol, returning Sienna, Magnus and Shaun to normal. Meanwhile, at the Sanctuary, the Grand Master summons the Gold Knights Aiolia and Milo to assassinate the Bronze Knights, who have defeated all the Silver Knights. While visiting the orphanage which is now for sale, Seiya is visited by Shaina who tries to warn him of the Gold Knights.

Having finally completed his research on the Knights and perfected the armors for the Black Knights, Vander Guraad assembles his army with the intention of killing Sienna and ensure the prophecy of mankind's downfall never comes to pass, as well as kill every other god. On Guraad's orders, three Black Knights ambush Seiya and Sienna while on a walk, abducting Sienna and bringing her to Guraad. While Guraad confirms to Sienna that Alman has died, the Bronze Knights ambush the compound, battling the Black Knights as they attempt to reach Sienna in time.

Sienna successfully destroys the Cosmo canister before fleeing with Seiya as the entire mountain compound begins to crumble from the explosion. Rendezvousing at the helipad, the Bronze Knights are locked in a desperate struggle against the Black Knights until Mylock arrives. Despite their victory, Sienna is saddened by the realization that her grandfather is truly gone while the Bronze Knights discuss her burden as Athena. Just then, their helicopter is attacked and crashes into the mountains. Upon exiting, they are confronted by Guraad in his own Black Knight armor. Despite outnumbering him four to one, the Bronze Knights are easily defeated one after the other, until only Seiya remains standing.

At the Five Ancient Peaks, Old Master is visited by the Cancer Gold Knight Deathmask who has been sent from Sanctuary to assassinate him, who is revealed to be the Libra Gold Knight Dōko who has refused the Grand Master's summons. Deathmask's attempt to send Dōko to the Underworld is thwarted by the arrival of Mū, revealed to be the Aries Gold Knight. After Deathmask departs, Mū informs Dōko that Athena has been shot by a god-killer arrow and is dying. Uncertain of whether to trust Dōko or the prophecy, Mū returns to the Sanctuary. Meanwhile, the Bronze Knights are attacked by the Silver Knight Sagitta Tremy, who fired the first arrow that pierced Sienna. Seiya overcomes Tremy's attack and defeats him. Just before dying, however, Tremy warns them that they only have 12 hours to remove it and the Grand Master is the only one capable of doing this.

Seiya attempts to fight Aldebaran but is easily overwhelmed by his speed. Failing to understand why someone with so much power will serve the Grand Master, Seiya attempts to make Aldebaran realize his errors. Aldebaran, who has seen the Grand Master as a benevolent man willing to personally visit a dying soldier and ease his pain, fails to understand Seiya's statement of him being evil. Instead, Aldebaran attempts to convince Seiya that the reason is because of the dark prophecy the Altar Silver Armor has foretold of Athena's current reincarnation. Attempting to finish the fight in an instant, Aldebaran attacks Seiya before burying him beneath the ground. However, Seiya remembers Marin's teachings about reaching the true potential of Cosmo, allowing him to return to the surface and continue his fight with Aldebaran.

At Andromeda Island, the Silver Knight Cepheus Daedalus, Shaun's master, is attacked by the Gold Knight Pisces Aphrodite on the Grand Master's orders. Despite putting up a fight, he is easily outmatched. Daedalus' other apprentice, Chameleon Genet who was originally sent away for her own safety, returns after sensing Daedalus' Cosmo fading. Before dying, Daedalus instructs her to go to Star Hill. After burying him, she encounters Marin who realizes that the Sanctuary battle has finally begun. It is revealed that Daedalus was aware of the evil lurking in the Sanctuary and had dispatched Shaun to fight in the Galaxian Wars in order to draw the enemy's attention, this being Dōko and Marin's reasons for sending Long and Seiya to the tournament as well. Relaying Daedalus' final words to Marin, Genet decides to accompany Marin when she decides to go to Star Hill in order to discover the meaning behind Daedalus' words.

During their childhood, Shaun and Nero wandered the streets, having not eaten for days. While going to get some bread for them, Shaun was attacked by feral dogs. In fear, Shaun accidentally awakened her Cosmo. This drew the attention of a pair of Sanctuary guards who had been sent to that town to discover someone with Cosmo. They attempted to abduct Shaun, but Nero fended them off before their superior, Guilty, confronted the siblings. Refusing to let him abduct Shaun, Nero attempted to fight him, awakening his own Cosmo in the process. Taking an interest in his Cosmo and anger, Guilty abducted Nero instead and retreated with him to Death Queen Island. Back in the present, at the House of Gemini, Shaun is saved by Nero's Cosmo attacking Gemini, disrupting the attack and allowing Shaun to see the exit. However, refusing to leave Magnus behind, and remembering Daedalus' words of there being a time when she has to fight for those she cares about, she instead returns to face Gemini, determined to defeat him at any cost. At that moment, Gemini scolds her for returning before informing her of Daedalus' death at the hands of Aphrodite. Her anger allows her to awaken her seventh sense, block Gemini's attack and successfully strike him, disrupting the illusion. Determined to avenge Daedalus' death, Shaun rushes after Seiya and Long.

Seiya and Long arrive at the House of Cancer, where they are confronted by Deathmask. Infuriated by Deathmask's collection of human faces, even children, decorating his House and his earlier attempt to assassinate Dōko drives Long into a vengeful fury, swearing to defeat Deathmask in the name of justice, while Seiya is ordered to continue to the House of Leo. All of Long's attacks are avoided and he's sent to the Underworld, where he regains his ability to see. Guided back by Sienna's Cosmo, Long resumes his fight with Deathmask, although he is overpowered and sent to the Underworld once again.

Long, with renewed fury, overwhelms Deathmask, swearing to kill him for having hurt Shunrei, the only person he truly loved. However, despite getting in several hits, Deathmask remains unscathed due to the protection from his Gold Armor, and he quickly gains the upper hand once more during their fight. Trying to appeal to the conscience of the Cancer Armor, Long eventually manages to reach it, as its leg piece detaches and Long manages to break Deathmask's leg before the remaining Armor completely abandons Deathmask. However, having pride as a warrior, Long discards his own Dragon Armor and faces Deathmask in a final clash of Cosmo, awakening his seventh sense and finally killing Deathmask by throwing him down Yomotsu Hirasaka. Returning to the world of the living, Long rendezvous with Shaun and discovers he now has his eyesight back.

Seiya's kick seems to have no effect for Aiolia except driving him into a frenzy, as he viciously strikes Seiya, breaking his leg in the process. Seiya is entirely at Aiolia's mercy until Cassios suddenly arrives. Cassios informs Seiya that Aiolia has been struck by the Demonic Illusion Fist and this is why Aiolia is nothing more than a killing machine. He can only be awoken if someone dies in front of him. To Seiya and Aiolia's surprise, Cassios pierces his own body, being willing to take his own life in order to have Aiolia awaken, as he realizes that Shaina would be sad if Seiya died. Having cared for her ever since she was returned to Sanctuary by Aiolia, Cassios came to realize that Shaina loved Seiya and wishes for nothing else but her happiness. Not wanting her to die in order to save Seiya, Cassios decided to go instead by knocking her out. Entrusting her to Seiya, Cassios succumbs to his wounds.

Shaun and Long arrive at the House of Leo, rendezvousing with Seiya. After healing Seiya's broken leg, Aiolia warns them about Shaka, instructing them to never let him open his eyes, or they are guaranteed to die. After they have left, Aiolia is confronted by Scorpio Milo, who has been there since Seiya entered the House. Admitting he admires the Bronze Knights determination although they are enemies, Milo confronts Aiolia about letting them pass through his House and decides to execute him for betraying the Grand Master. The Gold Knights are initially equal until Milo immobilizes Aiolia. Before Milo can continue, the Grand Master communicates with him through his Cosmo, instructing him to stand down.

Seiya attacks the skull Knight and blasts it apart. However, upon reassembly, it grows in size to a massive skeleton, rendering Seiya's attacks useless. However, Seiya manages to get close and crushes the skeleton, passing the test and being reunited with Long and Shaun who made it as well. Mū, Aldebaran, Marin and Genet finally arrive at the bottom of Star Hill. To Genet's annoyance, Kiki has arrived as well, having entrusted the care of Sienna to Mylock and wanting to help. After revealing a secret entrance, Kiki and the Knights enter Star Hill.

Genet, convinced that the Daedalus in front of her is real, is overjoyed to see her master alive and well but is attacked upon approaching him, to her and Kiki's shock. Attempting to fight back, Genet is easily overwhelmed and at Daedalus' mercy. However, her determination and wanting to help Shaun helps her overcome her doubt, and she overcomes Daedalus' attack and defeats him. At the House of Virgo, Long attempts to negotiate with Shaka to allow them to pass, due to his meditating pose not giving off any threatening presence. However, he strikes Seiya as he attempts to rush through, taking on the Bronze Knights and defeating them without any effort.

Despite being hit with Nero's Phantom Fist, Shaka is unfazed and instead reflects the attack to affect Nero's mind, showing him and an infant Shaun walking along the River Styx. Shaka tortures Nero and attempts to make him let go off Shaun to save himself from endless pain. Shaun manages to make Nero snap out of it, before she warns him about not allowing Shaka to open his eyes. Before the fight goes further, Shaun manages to break free and attempts to fight Shaka instead, but he knocks her unconcsious before removing Nero's Armor. Nero attempts to fight back but is burned to ashes. Just as Shaka believes the fight to be over, Nero emerges from the burning ashes with his Armor restored. Despite attacking four times in a row, Nero is unable to land a hit on Shaka who knocks him to the ground in an instant.

The Bronze Knights arrive at the seventh House, Libra, where they find Magnus encased in ice. Despite his best attempts, Seiya is unable to even scratch the surface of the ice. Just then, Long's master appears before them before summoning the Libra Gold Armor to help them. Long chooses the Libra sword which successfully shatters the ice and saves Magnus. However, there is no pulse. Seiya and Long keep moving, leaving Shaun behind to grieve Magnus.

Meanwhile, Mū, Aldebaran, Marin, Genet and Kiki reach the top of Star Hill. Just as they are about to enter the Grand Master's Temple, Mū notices the figure of the Grand Master collapsing. Before they are able to react, a powerful blast incapacitates Mū and Aldebaran, before the Grand Master appears before Marin, Genet and Kiki. Marin attempts to fight the Grand Master, but no-one except the Grand Master may freely use their Cosmo while at Star Hill, and he easily overpowers them before attempting to kill all three at once. At the House of Aries, the three Sanctuary guards from before arrive, now accompanied by Cerberus Dante, who survived his fight with Nero, to kill Sienna.