To investigate the killing of a former girlfriend, her child, and her congressman husband, former LAPD detective Nicholas Marten comes out of hiding and stumbles upon a secret, illegal bioweapons program.

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.