The world has become a slaughtering ground for the Crimson Denizens, mysterious beings from a parallel universe who thrive on the life energy of humans. These merciless murderers only leave behind scant remainders of souls called "Torches," which are mere residues that will eventually be destroyed, along with the very fact of the victims' existence from the minds of the living. In an ambitious endeavor to put an end to this invisible, hungry massacre, warriors called Flame Hazes relentlessly fight these monsters. One fateful day, Yuuji Sakai ceases to be a regular high schooler—he becomes trapped in a crevice of time and is suddenly attacked by a Denizen. Coming to his rescue just in the nick of time is a nameless hunter who seems no different from an ordinary young girl except for her blazing eyes and burning crimson hair. However, before Yuuji can learn anything more about his situation, he discovers that he has already been reduced to a Torch—merely a scrap of memory waiting to be extinguished.
Yuji's existence has disappeared on Christmas Eve after the events of Statue of Pride. Like a disappearance of a torch, all those who aren't engaged in the World of Guze have forgotten him including his closest friends and families. Shana and Kazumi still believe that Yuji exists due to the fact that their letters given to Yuji haven't disappeared. However it is shown that Yuji still exists but makes a contract with a Guze no Tomogara and takes the Serei-dens throne as the new leader of Bal Masque.
Shana receives a response letter from Sophie Sawallisch about her report. Her words have made Shana felt uneasy and questions herself. She was able to figure it out during her training. Meanwhile Yuji officially arises as the new commander of Bal Masque, as Bel Peol announces their ambitions to all Guze no Tomogara that are present in Serei-den. Keisaku receives a spell from Margery that allows him to sense a nearby Tomogara as he heads off to Outlaw's Tokyo Headquarters. On the train, he senses one but it appears to be in a train in the opposite direction. The other train arrives in Misaki City with Yuji getting off it.
Yuji returns to Misaki City. Satou, who found that a Denizen is at the city, warns Tanaka. He decides to get to the Haridan where he meets Yoshida, who also decided to go there after being warned by Shana. Yuji walks around the city, while reminiscing about all events that he took part since he found out he was not human anymore. He climbs the top of Misaki Bridge where he and Shana finally meet again.
Yuji and Shana finally meet as Margery and Wilhelmina come to see what is happening. Yuji reveals that he is indeed himself but also The Snake of Festival and that he has come to save Shana from her inevitable fate as a Flame Haze—to fight against Denizens until she burns out. Shana does not believe him and the three Flame Hazes fight with Yuji. He traps Wilhelmina and Margery in a ball of silver. Yuji explains to Margery that the Silver is a projection of her emotions. He is a mirror of her hate towards everyone who abused her and has done the things Margery secretly wanted to do to them on her behalf. She has a mental breakdown and starts hysterically crying. Meanwhile, Yuji is chasing Shana and they fight. In the end, he captures her and goes to the Haridan with Shana unconscious in his arms. He takes the Haridan and claims it is his property. Yuji reveals to Yoshida, after she asks him, that he returned her letter back to let her know he chose Shana. She then falls on her knees in shock. Yuji flies to the Serei-den with Shana in his arms.
Shana is kept captive. Later on, she learns that Alastor has joined Yuji. Meanwhile, in our world, Margery is in a coma and Eita can't wake her up, unless Keisaku comes back. Outlaw doesn't give any information or help to neither Eita about Keisaku or Wilhelmina about Shana. Shana seems to be erased from everyone's memories and Wilhelmina refuses to help the Outlaw in the war until she finds Shana and that's why they won't help her either. Meanwhile, Lamies meets Shana again and the other three masters of Bal Masque seem to have a secret plan.
Keisaku is held hostage by an Outlaw - Widened Eye of Incineration, Emest Flieder, who believes that this way he'll make Wilhelmina join them in battle. His partner, the Scatterer of Sparkling Light, Rebecca Reed, frees Keisaku and sends him back to Margery Daw with Wilhelmina's reports. Rebecca flies to Wilhelmina, who has been her ally for a long time, and Sophie Sawallisch makes Emest the commander of the Tokyo Outlaw Headquarters. Meanwhile, at the Serei-den, Shana wonders why she couldn't do anything against Yuji and why she was so scared when he tried to catch her. She remembers when her trainer, Shiro, told her that one day she will find the greatest power that can bring down anyone and anything and then he asks to her to hold his hand. Shana then remembers how every enemy she fought, held hands with someone and she recognizes the greatest power of love that lies on the palm of Yuji's hand. Suddenly, there's a loud noise and when Shana goes out, she sees dead bodies and above them - the Master Throne, Hecate. She responds that Shana is no longer needed.
Hecate feels that Shana is a threat to them and should be killed and proceeds to attack her, but Yuji comes and saves her. Meanwhile, Kazumi meets Khamsin and asks him about the meaning behind the Treasure that Pheles gave her, since her feelings towards Yuji are changed after he rejected her. Back at the Serei-den, Yuji opens the Divine Gate, through which he intends to go and bring back the Snake of the Festival's true body and change the world. He then takes Shana and the Trinity with him to announce his plans to all Denizens as they prepare for the war. Then he, along with Bel Peol, Sydonay and Hecate, go through the gate.
As the war begins all over the world, Yuji, the Trinity and other Denizens are on the path to Snake of Festival's self. All Flame Hazes prepare themselves for the war, Carmel goes into the sea to the fallen kingdom and requests the help of Shiro. Khamsin and Rebecca infiltrate the Serei-den and start attacking and destroying everything. Meanwhile, Shana is alone and with no powers, when she notices what's going on and then she takes the swords in her room in preparation to fight.
As the war continues, Shana fights her way to Nietono no Shana and is finally ready to battle.
Sophie Sawallisch comes to assist with a large army of armed humans. Shana breaks free and after a battle against a Denizen, which ends up with Shana furiously killing it, she comes to self-awareness as the ultimate combination of the Flame-Haired Burning-Eyed Hunter - the Flame Haze, and Shana - the human she became after meeting Yuji.
Keisaku comes back and awaken Margery and they confess their love to each other at last. She makes him as powerful as herself fearing that he wouldn't survive by her. Meanwhile, at the Serei-den, Shana, Wilhelmina, Khamsin and Rebecca enter the Divine Gate to fight the Trinity and the Snake of the Festival. Outside the Gate, in a blizzard, the war is getting extremely intensive - more and more Tomogara armies are coming but they're loosing against the Flame Hazes. Decarabia comes to the surface and starts a powerful attack but Sophie Sawallisch finds him and kills him, using a large amount of her powers. After a moment of comfort that the most powerful enemy has been destroyed, Sabrac joins the war and the snow from the blizzard turns into Tomogaras.
Wilhelmina, Caramel and Khamsin begin a long and hard fight against Sabrac, which seems to be impossible to win. Shana leaves them and meets Snake of the Festival, who has awakened his true form, and promises him to fight him, make him the person he used to be and to live in a perfect world along with him. She has realized that the two personalities of her weren't the Flame Haze and the person, but the one who would and the one who wouldn't fight for the dream of a perfect life. But both have one thing that asures the chance for this dream to be realized - the most powerful unrestricted spell, Love.
Inside of the Divine Gate, Sabrac falls, gazing at the greatness of the Snake of the Festival in his true form. The God of Creation then sends out a signal and starts moving towards the Divine Gate. After the signal is felt by everyone, Sophie Sawallisch attempts to destroy the Gate. At the last moment Fecor protects it and dies from the power of the spell. Back in the Gate, Shana and Yuji are fighting, while Yuji now looks as he was before. Because of a memory that vows between two people are sealed with a kiss on the lips, Shana kisses Yuji on the cheek and says that is her vow. She is then taken away abruptly by the ghosts of the Flame Hazes outside of the Gate as it breaks and the Snake of the Festival comes out. All Tomogara cheer and all Flame Hazes stand in astonishment and despair and amongst this, Shana recognizes this as a sound not of a fall, but of the start of a new battle.
The Flame Haze army retreats as the Snake of the Festival destroys their morale. He announces his plan to create a new world, a complete copy of ours, to be a paradise for Tomogara and with Power of Existence flowing everywhere. Thus, all Tomogara would leave the world and the Flame Hazes would stop fighting agaist them. After that, panic and chaos reigns among the Flame Hazes, who now don't have a purpose and the Tomogara attack them.
The Flame Haze army retreats to the Palace of Light with the help of the Gods of Earth and Margery Daw. Samuel sets up a decoy stalling the Denizens' advance and discovery of the Palace of Light.
The few surviving Flame Hazes decides whether to continue the fight or not. Sakai Yuji said that the Seirei-Den will head to Northwest, towards Misaki City where he will start the creation of Xanadu.
Shana makes it to New York, and meets up with the rest of the gods of Earth. They agree to help Shana fight, and she then explains the plan to them. Yuji visited Misaki City and found Kazumi Yoshida and Eita Tanaka. He came back to convince Yoshida to join him in building the new universe. While Yoshida, Tanaka and Yuji walk around town, Yuji explains his what he intendes to do. After a while of explaining, Yoshida finally agrees to help him.
Kazumi was taken by Yuji in Sereiden and Hecate was sacrificed to the Snake of the Festival and now Shana and Yuji locked in their own confrontation
Kazumi activated the Giralda and Pheles emerges in the amber wind
Marjery helps Carmel in her struggle to understand her new purpose. Shana continues her struggle with Yuji. Bel Peol tries to figure out Shana's plan as the tower is sabotaged from within. Shana attacks Yuji before he can master his unrestricted spell.
Shana reveals her plan: not to stop Yuji's goal to create a new world, but to alter the Denizens' ability to consume humans in it.
Shana sends Carmel to protect the Engaged Link. Shana and Marjery continue to fight Yuji and Sydonay. Sale takes out the Researcher at the last second. Khamsin falls. It is revealed that Shana's plan was to trap the Grand Order by sabotaging Bel Peol's backup plan, thus thwarting her strategy.
Yuji reveals that the tower was a fake. The God of Creation uses the Reiji Meigo to enact his plan at midnight. The God of Guidance is summoned, forcing everyone to listen to her words. The God of Creation initiates the Grand Order to open the gateway to Xanadu, and the Denizens begin to depart for it.
Johann and Pheles give up their existence to give way to a new form of life, they son, Justus. Many Flame Hazes also leave for the new world. Yuji intends to reverse all the damage the Denizens caused to Misaki City, including the return of Hirai, effectively undoing all the relationships that Shana has built with everyone.