Jin Mikuriya is the protagonist of the story and an ordinary high school student living alone while his parents are away for work. He is an art club member who has a particular sensitivity to the supernatural, specifically the ability to see the bug-like "impurities" that begin spreading throughout the town after a sacred tree is cut down.

In terms of appearance, Jin has a youthful and somewhat childish look. A distinctive physical trait is his pair of "idiot hair" antennae, which often stand up comically whenever he is shocked or surprised.

Personality-wise, Jin is frequently described as a normal, relatable teenage boy, avoiding common archetypes such as being a hot-headed idiot, an arrogant bastard, or a self-righteous hero. He has a snarky side, often acting as a "little miss snarker" despite taking himself fairly seriously. He can be short-tempered, but he also exhibits a notable "pureness," typical of a boy who is attracted to women but has never actually had a girlfriend. While he currently presents as a typical student, it is revealed that he acted up quite a bit during middle school due to a troubled past, though he was never a true delinquent.

Jin's primary motivation throughout the story stems from his accidental summoning of the goddess Nagi. Having carved a statue from a sacred tree, the statue breaks apart and reveals Nagi, a guardian deity who claims the tree was her vessel. Because her tree was cut down, impurities begin to threaten the town, and Nagi has lost much of her former power. Jin is compelled to help her deal with these impurities and support her quest to regain her strength and discover her identity. To facilitate her living with him and attending school, they concoct the cover story that she is his long-lost half-sister.

His role in the story is that of the grounded everyman who anchors the supernatural chaos. Unlike the goddesses and eccentric characters around him, Jin serves as the audience's point of view, often reacting with a relatable mixture of exasperation, humor, and concern for the absurd situations he finds himself in. His ability to see and physically interact with the impurities makes him a necessary partner to Nagi in her purification duties.

Key relationships define much of his experience. His bond with Nagi is the central axis of the story, starting with forced cohabitation and gradually developing into a deep, albeit complicated, connection that hints at romance. He also has a childhood friend, Tsugumi, who has a secret crush on him and often finds herself jealous of Nagi's sudden intrusion into his life. His dynamic with the other goddess, Zange, is more antagonistic and playful, as she attempts to seduce Jin away from Nagi to gain an advantage in their sibling rivalry. At school, his friends in the art club include the genre-savvy otaku Meguru Akiba and the shy, intimidatingly large but gentle Daitetsu Hibiki, providing regular comedic support.

Throughout the narrative, Jin experiences significant development. Initially just a boy dealing with a bizarre situation, he becomes emotionally invested in Nagi's well-being. When Nagi runs away during a crucial moment of crisis, Jin suffers a severe emotional breakdown, showcasing his deep reliance on and care for her. This moment forces him to confront his feelings and move from a passive participant to someone actively fighting to resolve the supernatural conflict affecting them.

Jin possesses a few notable abilities. His primary supernatural trait is his sensitivity to impurities, which allows him to see them when normal people cannot. More importantly, he has the unique physical capability to touch and directly handle these impurities, a necessary function for Nagi to purify them with her magical-girl-style wand. Beyond these supernatural talents, he is also a competent cook, often preparing meals for himself and Nagi, as she generally finds the task too bothersome.