Even as butterflies ominously proliferate in town, the rumour of a mysterious creature lurking in the tunnel behind the school spreads among the children. When the body of Arie Kimura's mother is found by this tunnel's entrance, next to apparently human traces, the legend seems to be confirmed. Is the end of the world coming? In order to appease the wrath of the beast, the children decide to offer it a sacrifice: The unfortunate Arie, whom they believe to be the cause of the curse, is shoved into a well that leads to the Nijigahara tunnel—an act that in turns pushes Komatsuzaki, the budding thug who has carried a torch for Arie for a while already, entirely over the edge.

But this is only the beginning of the complex, challenging, obliquely told Nijigahara Holograph, which takes place in two separate timeliness and involves the suicidal Suzuki; Higure, his stalker-ish would-be girlfriend; their teacher Miss Sakaki, whose heavily bandaged face remains a mystery; and many more―brothers, sisters, parents, co-workers, teachers, aggressors and victims who are all inextricably linked to one another and all will eventually―ten years later―have to live with what they've done or suffered through.