One year ago, Aika Fuwa and her parents were murdered under mysterious circumstances. Swearing vengeance on her killers, Aika's older brother, Mahiro, sets out to determine who ended her life prematurely. Unbeknownst to Mahiro, his childhood friend and Aika's secret longtime boyfriend, Yoshino Takigawa, ends up getting dragged into the investigation after being held at gunpoint by a strange woman. Yoshino learns that Mahiro is being investigated by the government after outbreaks of a mysterious "iron sickness" in two locations where he was previously seen. Now on the run, Mahiro and Yoshino's search for Aika's killers becomes harder and more dangerous.

In an effort to find a lead on his sister's murder, Mahiro strikes a deal with Hakaze Kusaribe, the most powerful sorceress in the world who is imprisoned on a deserted island. As princess and leader of the Kusaribe Clan, Hakaze promises to aid Mahiro's investigation if he can rescue her from internment. Once free, Hakaze intends to put a stop to the revival of the "Tree of Exodus" and save the world from eventual ruin. Believing that Hakaze will get in the way of his resurrection plans, Samon Kusaribe, Hakaze's former aide, had orchestrated her banishment and removed her ability to use magic on the island.

In a desperate attempt to save the world from the effects of the "Trees of Exodus and Genesis," Mahiro and Yoshino inch closer to the truth behind Aika's death. The two find that there might be more to her murder than they initially thought as the world around them falls into chaos.