Fifteen-year-old twins Sophie and Josh Newman continue their magical training in Paris with Nicholas Flamel, Scatty, and the Comte de Sant Germaine, pursued by Doctor Dee and the immortal Niccolo Machiavelli.

After fleeing to Ojai, then Paris, and escaping to London, Josh and Sophie Newman are finally home, and after everything they have seen and learned in the past week, they are both more confused than ever.

Fifteen-year-old Josh has chosen to side neither with his twin sister Sophie nor with the Alchemyst, Nicholas Flamel, but rather to fight alongside Dr. John Dee and the mysterious Virginia Dare, while the immortal Machiavelli and Billy the Kid follow the Elders' plans to set loose the monsters of Alcatraz on San Francisco and trigger the end of the humani race.

Pulled through a glass that brings him back in time, Septimus Heap becomes the apprentice of an alchemist.