The story begins with Kotori Monou (who has an old childhood friend, Kamui) having a dream that she was in the classroom listening to her teacher talking about a story, until a girl in her class drops her pen and Kotori picks it up and gives it to the girl. Then Kotori 's teacher asks Kotori to read a passage in the story!! She reads for a minute or two and sees Kamui outside, walking to the school with a smile on his face!! Suddenly, Kotori awakens and realizes it was just a dream. She finds herself trying to get dressed and get ready for school as Fuma, her older brother, waits for her on his bike.

Kotori recalls her memories with Kamui as children, wondering why he has changed. Meanwhile, Kamui deals with people trying to attack him. While Kamui tries to recover from an injury, a Dragon of Heaven, Sorata, and a Dragon of Earth, Yuto, confront each other in hopes of meeting Kamui.

Kamui recovers under Fuma's and Sorata's care, but when Sorata questions Kamui's motivations for returning to Tokyo, he is quickly rejected by Kamui. Meanwhile, the Dragons of Earth begin researching to see if Kamui is the 'one'. Kamui encounters Fuma where they recall the pledge they made in the past. Their time is interrupted when the Divine Sword is stolen from the Togakushi Shrine.

Kamui meets his aunt Tokiko and learns of his mother's true fate. Arashi is attacked by the same people that attacked Kamui.

While trying to find the Diet Building, Yuzuriha bumps into a mysterious man who can see Inuki. Princess Hinoto shows Kamui her visions of the future and tells him of his destiny.

Sorata reflects on his past, growing up on Mt. Kouya. He recalls the destiny which the Stargazer told him. Kamui tries his best to be around for Kotori and Fuma, while their father is in the hospital. Satsuki plans an attack on Sorata and Arashi.

Satsuki recalls her past with computers when a mysterious organization began chasing her. She remembers how she found out about being a Dragon of Earth and meeting Kanoe for the first time.

Fuma's father leaves him a puzzling message before he dies. At the funeral, Kamui in confronted by Karen, a Dragon of Heaven, who has a letter from Kamui's aunt. Afterwords, Kamui and Kotori are dragged into the illusions of Seishiro. However, it is Fuma who saves them, but something is changing about that kind-hearted boy.

Yuzuriha and Saiki search for Mr. Aoki, but Yuzuriha meets Kusanagi, the man who could see Inuki. Yuzuriha tells him about her and Inuki, and why nobody can see him. Later, Yuzuriha catches up with Saiki and Mr. Aoki.

Kamui awaits Tokiko's arrival at the Togakushi Shrine. He recalls his past after he left Tokyo. But when Tokiko arrives injured, things take a terrible turn.

Kamui finally chooses which side he wishes to be on, but it comes with a grave consequence.

Sorata, Arashi, Yuzuriha, and Subaru worry about Kamui after seeing Kotori's death. Subaru decides Kamui needs to break free from his pain. Subaru dives into Kamui's conciousness in attempt to bring him back to reality. After Subaru is injured and uses too much power to remain in Kamui's mind, Kamui returns to normal and ready to fight.

Both sides gather and prepare for the battles to come. Kamui says his farewells to Kotori.

Kamui and Saiki make amends for their previous arguments. However, the two must work together when Fuma attacks Tojo Pharmaceuticals in search of Nataku's life support data. Fuma quickly dispatches Kamui leaving Saiki to defend the collapsing building. Subaru steps in before Kamui is killed, but pays a serious price for his interference.