Arata Hinohara’s school life is terrible and he wishes he could disappear. Arata of Amawakuni must fight for his life after he is wrongfully accused of murder.

Accused of being the murderer, Arata is forced to stand trial. On the way he gets a chance to speak with his double.

Arata and Kotoha are taken to Gatoya, "the ultimate hell," where they are immediately attacked by two boys. A certain rumor has been spreading around regarding Arata, the alleged murderer of the princess.

In the modern world, Arata's family knows something is different about Arata, but they continue to try to converse with him despite their confusion. In Amawakuni, Arata is heading toward the Capital. Along the way, he learns of the relationship between the princess of Amawakuni and the Twelve Shinsho. He also encounters some nomads who say that, with the princess gone, the world will fall into chaos...

Ohika saves Arata after he collapsed during the party's travels. Shortly after, Akachi of the Twelve Shinsho arrives and orders Ohika to become his Zokusho. Ohika refuses as he has sworn his loyalty to Kannagi, but Akachi isn't content with taking no for an answer.

Still living in Hinohara's place back in the modern world, Arata meets Kadowaki at school and decides to "play" with him. Meanwhile in Amawakuni, Kotoha injures her foot on the way to the Capital and the party is forced to take a break in a ruined village. Alone with Arata, Kotoha works up the courage to make an unexpected move...

After learning of Kannagi's past, Arata is even more determined to change the world. He practices swordsmanship with Kanate as the party continues toward the Capital. Meanwhile, in modern Japan, Arata meets the friend who betrayed Arata and now feels immense guilt over what he's done.

Kadowaki has appeared in Amawakuni! Arata is confused, but after being bombarded with hateful words by Kadowaki, his emotional state changes. Later, stunned by the presence of Kadowaki and the change in Arata, Kannagi makes a powerful declaration. Arata is still hesitant, so Kannagi tells him...

Arata and the others have arrived in the domain of Yorunami, one of the Twelve Shinsho. Rather than meeting Yorunami directly, Arata decides to talk to one of his Zokusho first to learn what kind of man he is. The party reaches Suzukura, a city ruled by the Zokusho Hiruko, but are told that they are required to pay a passage tax to enter...

Arata and his party arrive at the palace, Tamayori, but Yorunami immediately uses his power to capture Kotoha. Arata pursues her and finds Yorunami himself within the palace. He challenges Arata to duel...

Kadowaki shows up yet again in the midst of Arata's battle with Yorunami. He tells Arata that he became a Sho for the sake of "fighting for submission," but Arata disagrees. The beliefs of Arata and Kadowaki, after crossing two worlds, are about to clash.