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.

Back in London, fifteen-year-old twins Sophie and Josh Newman must determine whom they can and cannot trust as they search for both Scatty and an immortal who can teach Josh the magic of fire, while Doctor Dee and Machiavelli continue to seek power.