"Shion" is a supernatural mystery anime set in a rural Japanese village surrounded by dense forests and ancient traditions. The story centers on Shion, a young girl who returns to her ancestral home after the sudden disappearance of her older brother, Yuuto. The village is steeped in folklore, with locals whispering about the "Hakutaku," a mythical beast said to appear during times of great calamity. As Shion investigates her brother's vanishing, she uncovers a series of eerie events tied to the village's history, including strange rituals, unexplained deaths, and a recurring pattern of disappearances spanning decades.

Shion's search leads her to interact with a cast of characters, each harboring secrets. Among them is Ren, a reserved boy who claims to have known Yuuto and offers cryptic warnings about the village's dangers. There is also Ayame, an elderly woman who serves as the village's spiritual guardian and holds knowledge of the Hakutaku legend. As Shion delves deeper, she discovers that the village's inhabitants are bound by a pact with the Hakutaku, trading sacrifices for protection. The narrative explores themes of guilt, sacrifice, and the weight of tradition, as Shion grapples with the moral complexities of the villagers' choices and her own role in the unfolding events.

The plot intensifies as Shion learns that Yuuto's disappearance is linked to the Hakutaku's resurgence, triggered by a broken pact. Flashbacks reveal Yuuto's involvement in uncovering the village's dark secrets, leading to his confrontation with the beast. Shion must navigate a web of deception, confronting both the supernatural entity and the villagers' complicity in maintaining the cycle of sacrifice. The story builds toward a climactic confrontation where Shion must decide whether to uphold the village's traditions or break the cycle, risking unforeseen consequences. The series concludes with an ambiguous resolution, leaving the fate of the village and its inhabitants open to interpretation.