The story begins in North America in the year 1929 and has two new main characters: A 16 year old New Yorker named Johnny Garland, and a 21 year old Native American woman named Shania, who has powers of fusion similar to Yuri and Kurando in the previous Shadow Hearts games. She makes pacts with spirits while Yuri and Kurando turned into demons. Johnny is a private detective and is hired by a name Gilbert to find a man named Marlow Brown, but when Johnny finds Marlow a "Window" opens up and a monster is let out. For the rest of the game follows Johnny, Shania, and company as they attempt to uncover the truth about Gilbert and his plans.