Sakurai Yuki was abandoned by his mother and left in an orphanage, where he spent his childhood alone. Now, as a high school student, Yuki has recently begun to have several mysterious dreams that leave him with a nostalgic feeling that he has seen it all before. In the evening he receives a letter from an unknown sender that leaves him worried by its contents. When he answers the cries for help of a fellow student, Yuki is almost hit by a truck but is saved by the quick actions taken by a mysterious silver-eyed man.

Yuki meets a man who introduces himself as Takashiro Giou, who claims to be his older brother and asks him to come with him to Tokyo. Yuki is initially confused by the sudden revelation and as a result (of the female Yuki accusing him of running away) causes his power to break the orphanages' windows. Later, he has a confrontation with Uzuki at school, and his powers almost goes berserk again. Frightened and confused at his growing powers, he runs away only to meet up with Zess who comforts him. As they begin walking, they are attacked by Duras or demons and are saved by Touko and Tsukumo, along with Takashiro who talks about the Giou Clan and how everyone of its members have special powers and that they need his power.

Yuki is troubled after his meeting with Murasame Toko and Tsukumo and Giou Takashiro, head of a family with special powers known as the Giou Clan. Does Yuki belong with Takashiro or with the children of the orphanage? Zess kindly watches over the confused Yuki while agents of evil approach. Zess warns Yuki to remain at the orphanage on Walpurgis Night but that night two orphans go missing and Yuki is asked to help look for them.

While searching for the missing orphans, Yuki receives a call from his classmate Uzuki and heads to school, where he finds someone unexpected. Worried for Yuki, Tsukumo uses his power to find him and heads to his rescue.

Having found his place among the Giou Clan, Yuki decides to travel to Tokyo with Luka and the Zweilt Guardians. On the way there, inexplicable feelings well up inside Yuki as Luka sleeps by his side. Meanwhile, the police bring a case thought to be the work of demons to Takashiro in Tokyo, and two new Zweilt Guardians await Yuki at the police station.

In Tokyo, Yuki and Luka wait for Takashiro as he makes a stop at a police station. A girl is attacked by a man whose identity is revealed to be nothing more than a golem, holding the girl hostage. The girl is then possessed by a Duras, who reveals her motive to about kill Yuki in exchange for being granted a wish. The Voice of God (a Zweilt Guardian) Hotsuma steps into the battlefield with his burning flame.

Yuki and the others finally make their arrival to the Twilight Mansion at dusk. Upon arrival they are greeted by Aya Kureha and Tachibana Giou, the steward and director of the mansion. Yuki is disturbed by the nostalgic feeling surrounding the mansion, almost as if he has seen it all before.

After everyone had breakfast at the Twilight Mansion, Tachibana Giou leads Yuki along with the Zweilt Guardians to the Communal bath which happens to be occupied by Toko Murasame and Aya Kureha. Luka drives Yuki to school in the morning. Outside the school, Kanata Wakamiya attempts to persuade Yuki to return with him but is interrupted by Toko's and Tsukumo's arrival. After the talk with Kanata, Yuki starts to doubt his decision to join the Giou clan. However, Luka reassures him that he should follow whatever he believes in, but suddenly three Mid-villains attack and attempt to capture Yuki.

Yuki notices a scar on Shusei’s chest and learns from Luka that some wounds—especially those inflicted by friends—cannot be healed. As Shusei’s condition worsens, the police inform Takashiro about eight missing high school boys, possibly linked to the Sleeping Beauty Syndrome. While walking Yuki home, Hotsuma recalls the bullying he faced as a child when others discovered his ability to create flames, leaving Shusei as his only friend. In the present, he learns his parents have abandoned him for money. Overwhelmed, he loses control of his power until Yuki comforts him and glimpses his past. Remembering the day Shusei stopped him from taking his own life, Hotsuma manages to extinguish his flames. Meanwhile, Shusei disappears, convinced he is no longer the one who can save him.

Takashiro orders the Zweilt not to look for Shusei as World's End is searching. Shusei wakes up in a strange place surrounded by the 8 missing high school boys. Ashley comes in and reveals herself to be behind the Sleeping Beauty Syndrome. She puts the infatuated girls into a fatal sleep to harvest the power of their emotions and keeps their desired boys for herself. The Zweilt find a video left for them asking for God's Light in exchange for Shusei's life. Meanwhile, Ashley tries to get information on the Zweilt out of Shusei, but puts him to sleep when he doesn't talk. Toko and Tsukumo go to the most recent girl's house to find any more clues on Shusei's disappearance. While Toko is inside, Tsukumo answers a call for help then is attacked by twin Opasts and nearly killed by Reiga.

With Yuki's help, Tsukumo wakes up long enough to warn the others of Reiga. Yuki, Luka, and Hotsuma set off to find Ashley and Shusei while Takashiro handles things at the mansion before catching up. The three enter Ashley's barrier, a suspicious amusement park where her stuffed dolls attack them. Luka takes care of them while Hotsuma and Yuki continue on. They run into Kanata, who tries to persuade Yuki to forget it and come back with him. Yuki declines and leaves Kanata. Hotsuma and Yuki finally reach Shusei, who appears to be lifeless.

Hotsuma fights Ashley, but can't keep up because of his injuries. Just as she's about to kill him, his shouts wake up Shusei who stabs Ashley. The two take her on with renewed strength from being back together. Just as they're about to kill her, the twin Opasts, Jekyll and Hyde, show up and turn the fight around in their favor. Luka arrives in time to kill Ashley, and save them. Just as they're about to finish off Jekyll and Hyde, Reiga appears. Yuki recognizes him as Kanata.

Yuki is shocked to see his childhood friend Kanata revealed as Reiga. While he struggles to accept that Reiga wants to kill him, the others rush to protect him. Shusei and Hotsuma take on the Opast twins, who have healed thanks to Reiga’s power, while Luka is kept busy by Fenrir, Reiga’s familiar beast. After defeating their opponents, Luka, Shusei, and Hotsuma hurry to Yuki’s side just as Reiga prepares to strike with icicle daggers. Takashiro arrives in time to shield Yuki, and both he and Reiga summon powerful beasts from their ancient books, which clash fiercely. Realizing Reiga hasn’t fully awakened, Takashiro overpowers his beast and injures him. Before Takashiro can finish the fight, Yuki stops him, begging Reiga to say their past memories weren’t lies. Reiga departs, warning Yuki not to believe everything Takashiro says.

After the end of the brief confrontation with Reiga, Yuki sleeps for two full days due to the shock he received at knowing that his childhood friend Kanata was in fact, Reiga. While the others worry about Yuki, he busies himself with house chores and helping around in the mansion in order to forget the pain of Kanata's betrayal. On the other hand, Shusei and Hotsuma reconcile with each other, promising that they wouldn't avoid the other again because of guilt while Tsukumo and Touko try to confront Luka about telling Yuki of his previous life. As Yuki mentioned that he would like to remember more about Luka, Tachibana approaches them and informs Yuki of Takashiro's request that Yuki visit the Kamakura residence to learn more about the past.

Yuki is set to leave for the Kamakura residence with only Luka and Tachibana. Though the others wish to join him, they eventually give in to Takashiro’s order that only Yuki should go to the Giou main house. Senshiro, a Zweilt-in-training from the main family, arrives to escort Yuki and his companions, stopping along the way to pick up his partner, Kuroto, a shogi prodigy who quit to focus on the battle. Upon reaching the main house, Luka tells Yuki he can’t enter because some there wouldn’t welcome him due to his being a Duras. Yuki reassures him of his determination to learn everything about his powers, the battle, and his past life, while Luka silently wonders if Yuki’s feelings will change after learning the truth. At the Kamakura residence entrance, Yuki is greeted by Fuyutoki, the Giou main house butler and older brother of Aya, who runs the Twilight Mansion. Yuki is then shown to a room, where Takashiro later arrives after completing a purifying ritual.

Takashiro invites Yuki to accompany him on a stroll through the gardens. Passing through a bamboo grove, Yuki feels a sense of nostalgia towards the place. When Takashiro winces in sudden pain, Yuki gets to know more about Takashiro's real self: Takashiro is harboring a Duras within himself, enabling him to heal his wounds and making him immortal and renewing his memories. Takashiro has actually lived for more than 1000 years and was present since the start of the battle. He proceeds to tells Yuki that he was not related by blood to Yuki and that it was a lie to gain Yuki's initial trust. The reincarnation of the Zweilt guardians are also due to Takashiro summoning their souls back into the world in order to participate in the battle. Receiving empathy and understanding from Yuki who assures Takashiro that he remains an important person to him even if they do not possess blood ties, Takashiro brings Yuki to a monument which is known as God's Stone, the source of the Giou family's powers. There, he explains the origins of Reiga who was born from a union between a Giou-clan mother and an Opast father, making him a forbidden child. Reiga's main intent is to destroy humans as he views them as not fit to live. Takashiro mentions that Reiga who was reincarnated as Kanata holds no memory of his past self before his awakening, assuring Yuki that the Kanata he has spent his childhood with is not a set up facade. Relieved, Yuki confronts Takashiro to reveal the event that causes Reiga to betray the Giou clan.

Takashiro recounts the events that took place 1000 years ago, during the Heian period. The Giou clan was a well-known family who directly served the court and was led by 4 high-ranking personages: Ario, Takashiro, Reiga and a girl named Yomi. Reiga was feared and shunned due to his mixed parentage but he was supported by both Takashiro and Yomi. They lived in relative peace until a summons came from the royal court for the Giou clan to exterminate some high-ranking demons that were accidentally summoned. Takashiro accepted the task and set off from the village, leaving Reiga and Yomi in-charge of defending the village. Before he left, however, he remarked that he would be back to witness the blossoming of the lone sakura tree (representing Reiga) which had not put forth flowers for a long time. The demon-exterminating task took Takashiro longer than he initially thought and as he rode back, he noticed a great fire devastating the village. Hearing from an injured villager that Reiga had disarmed the barrier that protects the village, allowing a horde of monsters to assault the place, he ran to Yomi's room but found her dead. He received the scar on his face as Reiga directed a beam of light while Takashiro attempted to rush to Yomi's side. As Takashiro questioned Reiga as to his motive for burning the village, Reiga remarks that "everything is already too late" before disappearing. Yuki, after learning of the event that ignited the battle, decides to continue participating in it to stop others from getting hurt. It is also revealed that Ibuki and Tsubaki are his aunts; them being his mother, Mizuki's younger sisters. Handing over a picture of Mizuki to Yuki, they reassure him that his birth was not meaningless as he is loved and wanted. It was unknown, however, why Mizuki withheld the name of her husband from her sisters and also the reason Yuki was left at the orphanage.

Yuki decides to visit Luka and is assigned Senshiro and Kuroto as his bodyguards by Takashiro. At Yuki's prompting, Kuroto reveals that he and Senshiro owe Luka a great debt. Meanwhile, Touko and Tsukumo secretly takes a train to the Kamakura mansion in order to check up on Yuki. While Yuki wanders around the compound outside the mansion searching for Luka, Luka encounters Elegy, a General-class Opast from his past, at a clearing within a forest. She tries to persuade Luka to return to the Duras' side but is rejected. A brief fight ensues with Luka easily disarming Elegy, most probably because she refuses to use her full power. As he is about to deal the finishing blow, a figure appears before him: the female Yuki from the past. Luka is stunned to see her and lowers his guard, embracing her as she repeatedly tells him that she loves him. The figure proved to be an illusion when Tsukumo injures Elegy with a shot from his gun and both he and Touko run up to Luka to provide back-up. Elegy, outnumbered, retreats. On the other side of the forest, Yuki is rushed back to the mansion by Senshiro and Kuroto after they sensed Elegy while searching for Luka. Yuki, however, remains worried about Luka's whereabouts as he enters the safety of the mansion.

Kuroto asks Yuki to play shogi with him, where Kuroto shares his past of how Senshiro becomes his second partner. Hotsuma and Shusei are summoned to the Kamakura residence.

Deeply concerned for his master Takashiro, Fuyutoki feels frustration with his inability to do anything but simply wait. Inspired by his words, Yuki disobeys Takashiro's orders and leaves the mansion to search for Luka. Meanwhile, Kuroto and Senshiro's nemesis Cadenza, who was summoned by Reiga, vigilantly watches for an opportunity to attack the Giou Clan. When Yuki emerges from the safety of the compound, Cadenza raises a barrier to trap him. Kuroto and Senshiro arrive in time to defend Yuki but are badly outclassed. Yuki raises a wall of defense around Kuroto, Senshiro and himself but starts to fail under repeated attacks from Cadenza. Reiga appears and deflects Cadenza's attack that would shatter Yuki's wall.

Reiga orders Cadenza to withdraw, binding him with summoner’s chains that Kuroto warns will burn if he resists. Cadenza notes that Reiga’s power is weakened by controlling two General-Class Opasts and easily breaks free, turning on his master as the “Master Killer.” Reiga is quickly overwhelmed, but Luka intervenes, blocking the fatal blow. He sends Yuki back with Kuroto and Senshiro, promising to protect Reiga if Yuki wishes it. As Luka and Cadenza clash, the other Zweilts join the fight. Cadenza then targets Yuki, but Reiga unexpectedly shields him. Yuki believes Kanata is still inside him, while Reiga insists Kanata is gone, prompting Cadenza to question where his master’s loyalties truly lie.

Reiga and Cadenza retreat to Infernus, granting everyone a temporary reprieve from battle. Having pushed the limits of his power, Yuki loses consciousness and collapses. Witnessing the damage Yuki suffered in battle, the Zweilts gathered at the Kamakura mansion renew their promise to end the war. The doctor warns Tachibana and Luka that if Yuki uses his power again while he still lacks control, Yuki will die. While Yuki and Takashiro are bedridden, Elegy gives Hyde, the surviving Twin Opast, her blood to drink, enabling him to power up. Then the three Opasts attack the Kamakura residence. The Zweilts put up a fight. When Yuki tells Luka he intends to join the fight, Luka goes in his stead, leaving Sodom to guard Yuki. However, Yuki is unable to remain behind in safety and forces himself to go to the fight. As Yuki summons his power to help the Zweilts, Reiga arrives and steals Yuki away, then the three Opasts withdraw.

Reiga kidnaps Yuki and uses him to lure Luka and the Zweilts into his territory. Takashiro discovers Reiga's whereabouts and sends Luka and the Zweilts to rescue him. Hyde is held back by Hotsuma and Shusei, Elegy is held back by Tsukumo and Touko, and Cadenza is held back by Kuroto and Senshiro, leaving Luka to confront Reiga and save Yuki. During the magical battle with Reiga, Luka is badly injured. Then Reiga blasts Yuki, intending to kill him, but Luze who addresses Luka as "older brother" arrives and stops the blast because his understanding was that Yuki is essential to their plans.

Reiga orders Luze, Luka's younger twin brother, to destroy everything that stands in their way, so Luze challenges Luka. During the fight of Luze and Luka, Takashiro breaks through Reiga's barrier and takes on Reiga, using the darkness within him (the Duras in his body) to put him on equal standing with Reiga. Yuki decides to summon his power to end the cycle and his power goes out of control. Reiga orders Luze to leave because when God's Light is unleashed, it dispels all darkness and can endanger a Duras' existence. Luze, Cadenza and Elegy flee God's Light while Hyde is destroyed and the Zweilts' injuries are healed. Yuki is unable to stop his power but Luka manages to save him. Luka, Takashiro and the Zweilts return to the Kamakura residence with Yuki. Takashiro says the prophetic ritual revealed no emergency, so it's assumed that there's no immediate threat from Reiga in the near future. Takashiro releases the Zweilts to live as they wish until the next battle.