The prologue is an excerpt from Nicholas Flamel’s journal, dated May 31 and written in San Francisco. Flamel calls himself “the Alchemyst” (vi) and states that his wife Perenelle has been abducted and his book stolen. He warns that without the book’s magic, they will both lose their immortality and evil forces called the Elder Race will prevail.

Fifteen-year-old Sophie Newman is on the phone with her friend Elle while working at The Coffee Cup when she spots an intriguing black car outside. Three burly, gray-skinned men and a smaller, dapper one come out, and Sophie has a feeling that the latter man looks at her from across the street. The men then enter The Small Book Shop, where her twin brother Josh works.

In the bookstore’s cellar, where he is looking for a book, Josh suddenly catches the smell of peppermint and rotten eggs. When he comes out of the cellar to investigate, he finds Nick Fleming, the shop’s owner, standing in front of four strange men, and the smell gets stronger.

Rather than speaking, Nick and the stranger face off by throwing balls of energy at each other that create explosions and make the books fly.