Kōshi, a 15-year-old former academy student from the capital celebrated for his exceptional intellect and special student status, faces hardship after his father Haijū—a fire hunter—vanishes under unknown circumstances. Orphaned by his mother's subsequent death, Kōshi must relocate with his chronically ill younger sister Hinako to the estate of wealthy industrialist Yuoshichi Okibi. Yuoshichi provides shelter and medical care for Hinako, afflicted by poisoning tied to the capital's industrial pollution, in exchange for Kōshi's scientific expertise. Yuoshichi tasks Kōshi with top-secret research: enhancing "bottled lightning," a fuel derived from fire fiend blood, to harness the volatile energy of "skyfire." This urgent project stems from Yuoshichi's prediction of the ruling Divine Clans' imminent collapse and an anticipated assault by the rebel Spiders faction, aiming to create a potent energy source or weapon for survival. Kōshi's path crosses with Touko, a village girl journeying to return his deceased father's belongings. Initially unaware of Haijū's fate, Kōshi uncovers links between his father's disappearance, Yuoshichi's ambitions, and wider political conspiracies. His investigation leads him to a clandestine library where he discovers a book containing suppressed historical truths about the calamity causing human combustion near natural fire. Red hairs found within prompt him to seek the fire hunter Akira, suspecting her missing brother authored the text. Progressing further, Kōshi allies with Touko and the tree folk—plant-like humanoids—to unravel the world's secrets. Through their elder Yanagi, he learns the origins of human combustibility and fire fiends, rooted in divine mismanagement. This knowledge places him within a prophecy concerning the "Flickering Flame," a millennial comet threatening Earth, and the rise of a destined "lord of the fire hunters." Kōshi's journey centers on protecting his sister, navigating treacherous political intrigue, and applying his scientific acumen against existential threats. His actions help expose the Divine Clans' secrets and the Spiders' plans, positioning him as a crucial figure in the struggle to avert apocalyptic destruction.