Kanokon follows Kouta, a boy from the countryside who leaves home to live with his grandmother and attend high school in the city, determined to start over as an ordinary student. That plan falls apart almost immediately when Chizuru, a beautiful fox spirit, decides that Kouta belongs to her and refuses to leave his side. Her relentless pursuit is only the first sign that his new life is about to be dragged into the supernatural. Nozomu, a wolf spirit, soon enters the picture, and before long other youkai begin showing up with their own interest in him.
Between classes, family expectations, and the constant attention of spirits from beyond the human world, Kouta can barely keep up with the absurd situations around him. What should have been a quiet school life turns into a parade of misunderstandings, flirtatious clashes, and increasingly outrageous encounters, with Chizuru pushing forward, Nozomu complicating matters, and the rest of the supernatural cast making normalcy impossible. Kanokon blends romantic comedy with supernatural mischief into a story about one unlucky boy trying to survive a city life that keeps becoming stranger by the day.