In this novel, Susan Kay reimagines Gaston Leroux's famous novel The Phantom of the Opera in greater depth and detail. Phantom begins with a young widow giving birth to her only child. The child's face is severely deformed, and despite the signs of genius he shows from his early days, she cannot bring herself to love him. The child, Erik's, childhood is spent longing for the love of a mother whose only gift to him was a mask.

Eventually Erik runs away and joins a circus freak show. The cruel owners capitalize off his hideous face and his hauntingly beautiful singing. After leaving the circus, Erik becomes an apprentice to a stone mason, and experiences an adolescent crush on the mason's daughter, but after his appearance inadvertently causes a terrible tragedy, he escapes once again, this time to Persia, and the queen's court. Finally, tired of the world's rejection, Erik helps to design the Paris Opera House, complete with a cavernous and labyrinthine basement, where he intends to live out the rest of his days. It is here that he encounters, Christine, a young soprano with whom he falls in love.