One day after school, Yuji Sakai is thrust into a battle between two Rinne and a Flame Haze of the Crimson Realm. After the battle, he discovers that he is already dead.
Yukari Hirai's flame after becoming a Torch is about to go out already. With not much time left, Yuji tries to make her last moment on Earth memorable.
With Yukari Hirai already disappeared, Shana joins Yuji's class in her place in order to keep an eye on him. While at school the next day, the same Rinne from before attacks Shana once more.
Shana unexpectedly starts living in Yuji's house for the time being. Later, another Flame Haze by the name of Margery Daw comes to Misaki and starts a battle with Shana.
While on a date with Kazumi at the art museum, Yuji meets Lamies the Corpse Retriever who has been eating many of the Torches in town whose flames are all but burnt out. Meanwhile Margery Daw has a run in with Friagne the Hunter.
Friagne decides to accelerate his plans and begin the City Devouring process sooner rather than later. Shana must go and find some way to defeat him before it's too late.
Yuji has requested that Shana start to train him for future battles as he believes he may be of some help to her. Margery Daw is still on the trail of Lamies with the intention of ending his life.
The battle between Margery Daw and Shana has finally begun while the fate of the entire city rests in the balance. What can Yuji do to help Shana during battle?
Due to it being so hot outside, Hayato Ike hands out tickets to a water park and ultimately it's decided that Yuji and his friends go there after school. Once there, Margery Daw unexpectedly shows up, though Shana can't sense any intent to kill.
Yuji's training is not going so well so Shana wants to up 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 Yuji are growing stronger and now Shana asks Yuji's mother for advice about the meaning of a kiss. Also, two more Denizen are on a search for Shana.
After seeing Yuji and Shana together at the river one night, Kazumi's feelings for Yuji are hitting the breaking point until she finally confronts Shana about it. Suddenly, the two sibling Denizen show themselves and Shana rushes into battle.
Shana finds a way to somehow get out of the clutches of the two incestuous Denizen during their battle. Meanwhile, Yuji gets help from Margery Daw to help destroy them as well.
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 is also a Flame Haze.
With Tendo-kyu, the castle Alastor and Shana resided in, destroyed, the time has now come for Shana to finally become the Flame-Haired Burning-Eyed Hunter. However, she must first enlist the help of Tenmoku Ikko, a very powerful Mystes.
The Misago Festival is coming soon and Kazumi has made up her mind to confess her feelings there. However, she meets a new Flame Haze who tells her the truth about the world.
When Yuji doesn't come home after school on the day of the festival, his mother and Shana go to the festival to look for him but before long another Denizen shows itself. Also, Kazumi discovers the truth that Yuji is indeed a Torch.
The Seeking Research Denizen has already started his plan to open up a gate to another dimension and now all three Flame Haze must work together to defeat him.
Wilhelmina arrives in Misaki and meets up with Shana again. Meanwhile, Margery Daw finally leaves without saying goodbye to Eita or Keisaku. Wilhelmina comes to the conclusion that Yuji must be destroyed in order to protect the balance of the world.
Shana is able to persuade Wilhelmina, at least for now, to not destroy Yuji, who has finally decided to leave Misaki in order to protect it. Later at the bonfire which burned much of the decorations from the festival, a spell is activated.
After getting heavily injured, Shana must recover in the care of Wilhelmina. Meanwhile, Hecate begins to synchronize with the Reiji Maigo residing within Yuji.
While fighting within the Seirei-den, a spell is cast which drains their power of existence for a time, however, Margery Daw comes back and destroys the spell. Ultimately, it is now up to Shana to decide the fate of Yuji.
After managing to defeat Hecate, the city is about to be destroyed regardless. However, there is one final plan, though Shana's life may be on the line if it succeeds. Shana then confesses her love to Yuji, thinking that she would die.