Soul Hackers takes place in the fictional Amami City, a technologically-advanced Japanese metropolis. The main protagonist, a member of a hacker group called the Spookies, gains access to the closed beta for Paradigm X, an online game designed to connect the citizens of Amami. While in there, the protagonist encounters supernatural forces, then must work with the Spookies to investigate attacks by demons across the city. Aiding him is Nemissa, a demon who possesses the body of his friend Hitomi Tono.