Soul Hackers takes place in Amami City, a city fully connected through a colossal electronic network. The protagonist is a young man that belongs to a group of amateur hackers called the Spookies. While using his skills to hack his way into getting a beta invite for the new virtual world Paradigm X, he makes contact with a mysterious being named Kinap. Through a series of vision quests, the protagonist learns the secrets behind Paradigm X and the actions of a group called the Phantom Society that are working to steal souls through it.
He and his friend Hitomi Tono, who has been possessed by the demonic entity known as Nemissa, work together with the Spookies to put a stop to the Phantom Society's plans.