The game centers around two original characters; Arisu Reiji and Xiaomu, agents of a secret organization known as "Shinra", who deals with supernatural occurrences. Before the game's story, Shinra stopped a plan from the "Ouma" organization to create "fluctuations" to open up portals between worlds, albeit at the cost of Reiji's father life. Ten years later, Reiji and Xiaomu are investigating new fluctuations happening in Shibuya, Tokyo; and soon discover that characters and locations from different worlds and times are converging together, and "Ouma" agent Saya, related to the death of Reiji's father, is involved.