The game´s storyline continues directly from where the first one ended. The game focuses on EVAN SELWYN, the slightly UTR party member from Onyx 1. With the help of nine other young warriors, Evan succeeded in destroying the Onyx, not only saving Allumia and Earth, but dimensions all over. After returning both worlds to normal, Evan has moved on with his life. He settled down with girlfriend CHLOE ANDERSON, and remains close with old friends ZEDEKIAH CAMPBELL and VICTORIA TAYLOR. Between the fame and the money, Evan´s life has been perfect....until recently.

Three months ago, a series of cult-related murders began taking place all over Allumia, beginning in Trace Avenue, and rapidly spreading throughout. In Reyme, missing teenagers are found dead and many more are being kidnapped, with little clues as to who is committing these crimes, and the motive behind it.

Meanwhile, on Earth, lately JADE LUAN has had a nagging feeling that something is not quite right. She cannot quite put her finger on it, but she believes that her world is "missing" something, as if something was purposely removed from it. She feels that her eyes are decieving her, and while friend and former ally NICOLE SILVER feels the same, she chooses to ignore it.

In Allumia, Evan, Chloe, Zed and Vicki decide to see Enzan´s yearly talent show. Once there, Evan is attacked by a strange pale-faced teenager, who claims to know him from long ago. Suddenly, Evan sees flashbacks of a "teenager in red", however he does not remember meeting such an individual.

The pale-faced teenager runs off, and not before long, demons begin appearring all over the world. Pieces of the Onyx resurface, once again becoming an object of pursuit for many supernatural forces. Forced out of his comfort zone, Evan is pushed into the leadership position. However...things are now different. If the Onyx is regain shape, its power will increase tenfold, the worlds will merge to form Vereor, Genna and Baal will return to life, and a powerful entity, said to be the "true" creator of mankind, and will be released from his cage, and will regain control over the reality he originally created.