Josh has chosen to side neither with his twin sister Sophie nor Nicholas Flamel, but rather to fight alongside Dr. John Dee and Virginia Dare, while the immortal Machiavelli and Billy the Kid plan to set loose the monsters of Alcatraz on San Francisco.

Nicholas Flamel and teenaged twins Josh and Sophie Newman return to San Francisco where a weakened Flamel reunites with his wife, Perenelle, hoping to use his remaining power to prevent the monsters on Alcatraz Island from escaping. Meanwhile, Dr. John Dee and Machiavelli continue to seek power and the twins desperately try to determine who they can trust as they search for Scatty and an immortal who can teach Josh the magic of fire.

Soon after moving to Noble's Green, Pennsylvania, twelve-year-old Daniel learns that his new friends have super powers that they will lose when they turn thirteen, unless he can use his brain power to protect them.

When witches steal Tom's inheritance and kidnap his relatives, Tom, the Spook, and Alice set out for Pendle Hill, a particularly dangerous district, in hopes of preventing the three witch clans from uniting to raise the Fiend, the Devil himself, thus bringing about an age of darkness.

Seventh-grader Molly has always been an outsider, even at New York City's elite Metropolitan Institute of Science and Technology, but that changes when she is recruited to join the Omegas, a secret group that polices and protects zombies.

With the twins of prophecy split, Nicholas Flamel near death, and John Dee in possession of the swords of power, Danu Talis has yet to fall and the future of the human race lies in the balance.