It was a normal day in the life of Sakai Yūji, a 15 year-old highschool student, but then all of a sudden his life changed. When a Monster called "Guze no Tomogara" attacks him and everyone around him, turning them into blue flames and consuming them, Yūji's life gets saved by the Flame-Haired Burning-Eyed Hunter. A girl in a black coat, flaming red hair and a long sword, whom he would later name Shana. Confused and seeking answers Yūji follows the girl and finds out the harsh truth about everything around him.

Shana has come to the conclusion that Yuuji is restricting her role as a Flame Haze and is forced to make terrible decisions. Just when she is about to carry out her decision, Friagne begins to make his move on his City-Devouring plans. Can he be stopped in time?

With Tendo-kyu, the castle Alastor and Shana resided in, destroyed, the time has now come for Shana to finally become the Flame-Haired Scorching-Eyed Slayer. However, she must first enlist the help of Tenmoku Ikko, a very powerful Mystes.

Shana manages to return all beat-up from her previous battle with Margery Daw, and she's way too angry to receive help from the concerned Yuuji. Because there's nothing he can do, Yuuji goes to school, only to be greeted by a girl, Kazumi who asks him out on a date. However, on their date, Yuuji runs into a mysterious man who's been erasing Torches.

Due to it being so hot outside, Hayato Ike hands out tickets to a water park and ultimately it's decided that Yuuji and his friends go there after school. Once there, Margery Daw unexpectedly shows up, though Shana can't sense any intent to kill.

Back before Shana became a Flame Haze, she was living in a large castle-like structure floating in the sky along with Alastor and a maid who cares for her. One day, a Denizen attacks the maid, whose name is Wilhelmina Carmel, who also happens to be a Flame Haze.

Yuuji and Shana seem to be getting along well and she unexpectedly sleeps over, in his room. The problem is that Shana starts to feel differently about this Torch (Yuuji) than any other, could she be developing feelings for him? Meanwhile, another Flame Haze arrives in the city. What is this person's motive?

The girl with flaming hair uncovers the truth about the world that Yuuji is living in. He learns that he is already dead, and is only lasting until his flame burns out. As he watch his classmate's flame about to burn out, Yuuji felt useless for doing nothing and wants to help. He tries his best in making an effort of giving her a good time before she leaves...

Margery Daw and Marchosias continue to search for Rammie, with Shana and Yuuji right behind them. As they continue to chase Margery, Shana and Yuuji hope to give Rammie a chance to get out of Misaki and to allow him to travel some place farther. Yuuji also wants to fight alongside with Shana. With that, Shana begins to train him for future battles.

Ike suggested to visit the amusement park as a welcome for Konoe, but the carefully planned outting turns out all wrong when he miscalculated certain events. His underlying plan of impressing Kazumi was believed to be ruined initially, but he resorted to asking Kazumi to ride the Ferris wheel with him, which he was confident he would not get sick in. But mid way through the ride, he got sick. The ending dedicates Konoe thanking Ike for the outting. With Kazumi giving a smile to Ike, he ends off his unlucky day.

A mysterious man appears near Yuji's home, and is spotted by Shana when he is following her and Kazumi. Shana instead plans to ambush the suspicious man, and afterwards attempts to kick the suspicious man. He manages to dodge the attack and is revealed to be Yuji's dad. Yuji's father and mother give advice to Shana and Kazumi about their affection towards Yuji.

The culture festival is approaching, and everyone in school is putting finishing touches in preparation for it. Shana's friendship with Kazumi becomes closer. Wilhelmina returns back with the research on the Reiji Maigo and she meets up with Shana and Yuji to explain its origins. It is revealed to be a treasure created by Pheles to ensure that her lover Johan would not die and stay with her forever. However, the pair was defeated somehow and the Reiji Maigo was lost, later being teleported inside Yuji. Wilhelmina warns Yuji and Shana to be on their guard against the possible return of Pheles to hunt down the Reiji Maigo.

The Destructive Blade, Sabrac appears from the explosion that engulf Yuji and everyone else. The overwhelming roar of flames covers Misaki city. Even with heavy wounds, Wilhelmina still faces her nemesis Sabrac.

Shana and Kazumi decide to write letters to Yuji, professing their feelings toward him through written words. Hecate suddenly appears and removes the Reiji Maigo from Yuji.

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.

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.

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.

Yuuji gave the "Flaming-hair" girl a name, and that name is "Shana". The next day, Yuuji went to school looking all depressed. He heard his friend talked about the girl that disappear yesterday and became excited because his friend remembers her. Everything changed when the classroom was attack by a Tomogara. Suddenly, Shana came out of nowhere. In order to save the people around him, he must sacrifice some of his torch power to turn everything back to normal. But will Yuuji do so?

Yuuji's training is not going so well so Shana wants to increase the level by creating a Fuzetsu one day after school. However, school business with the student council doesn't allow him to do this, so Shana gets angry at him. Also, another Rinne appears.

Shana's feelings towards Yuuji are growing stronger and now Shana asks Yuuji's mother for advice about the meaning of a kiss. Also, two more Denizen are on a search for Shana.

Shana finds a way to somehow get out of the clutches of the two incestuous Denizen during their battle. Meanwhile, Yuuji gets help from Margery Daw to help destroy them as well.

Now that she's become a Flame Haze, Shana must defeat Tenmoku Ikko and take his sword - Nietono no Shana.