It was a normal day of the life of Sakai Yuuji. When all of the sudden his life changed. When a Monster called "Tomogara" attack him and everyone around him. He was they confused and shocked because everyone around him was turned into a blue flame and being consumed by the monster. Yuuji's life was then saved by a girl in a black coat, with Burning Eyes (Also Known as Shakugan) and a flaming red hair holding a long sword. Due to the confusion and chaotic mess, yuuji got into. He follows the girl with flaming red hair and finds out the truth about everything around him.

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...

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 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?

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.

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?

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.

The battle between Margery Daw and Shana has finally begun while the fate of the entire city rests in the balance. What can Yuuji do to help Shana victor the battle?

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.

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.

After seeing Yuuji and Shana together at the river one night, her feelings for Yuuji are hitting the breaking point until she finally confronts Yuuji 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, Yuuji 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 also happens to be 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 Scorching-Eyed Slayer. However, she must first enlist the help of Tenmoku Ikko, a very powerful Mystes.

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

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 Misaki without saying goodbye to either Eita or Keisaku. Also, 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.