Sophie and Josh Newman are 15-year-old twins who are working at their summer jobs in The Coffee Cup in San Francisco (Sophie works at The Coffee Cup, Josh works at the bookstore on the other side of the street) when a mysterious man,
John Dee, comes into the bookstore for a book, the
Codex – or
Book of Abraham the Mage. Josh witnesses his employer, Nick, and Nick's wife Perry both using
magic. He discovers that Nick is not an ordinary bookseller, but is the medieval and the legendary alchemist, Nicholas Flamel, being kept alive by making the
elixir of life (a secret from the
Codex) for him and his wife,
Perenelle. Dee also uses magic and takes the
Codex by force while Josh is holding it – resulting in two pages being left behind; "The Final Summoning" pages that Dee needs to raise the Dark Elders, the beings whom Dee serves, and who have kept him immortal for several hundred years. Both Flamels need the
Codex to make the elixir of life, or they will age rapidly and die within a month. Also, if they do not retrieve the
Codex, Dee will summon the Dark Elders to destroy the world and return to an age in which humans are but slaves and food. Flamel quickly takes Sophie and Josh to a hideout to enlist the aid of
Scathach, a powerful Next Generation Elder. There, they are forced to run, threatened by rats sent by Dee, which is thwarted by Flamel and Scathach. Chased again almost immediately by tens of thousands of birds, Flamel then leads the twins and Scathach to secure the aid of
Hekate, a powerful three-faced Elder, who can awaken the twins' magical potential. Dee discovers this, and enlists the aid of
Bastet and the
Morrigan. The trio mount a massive assault on Hekate's
shadowrealm, to destroy
Yggdrasill – the world tree – that is the heart of Hekate's power. While Yggdrasill is attacked, Hekate awakens Sophie's magic abilities but does not have time to awaken Josh, as the tree has been set on fire by Dee. While she rushes to defend her home, Scathach, Flamel, and the twins attempt to escape the shadowrealm. While escaping, they encounter Dee and witness the power of the ancient Ice Elemental sword,
Excalibur. They see Dee transform a wereboar into pure ice, then shatter the statue. Scathach remarks that she thought that Excalibur had been lost when
Artorius died. The twins, Scathach, and Flamel escape the shadowrealm, shortly before the destruction of Hekate, Yggdrasill, and the entire shadowrealm. As they escape, Dee uses Excalibur to freeze the tree, and Hekate, whose life and power is linked to it, transforms to ice as well. As this occurs, Dee is informed that the Flamels and Scathach have escaped with the twins. In his rage, he shatters Yggdrasill, which crushes Hekate into dust, killing her. Flamel, Scathach, and the twins travel to Scathach's grandmother, the
Witch of Endor (also called "The Mistress of Air"), who teaches Sophie her magical secrets quickly by giving the girl all the witch's knowledge and the power to know how to use air magic. While they are there, Dee has found out that a
prophecy in the
Codex speaks of Sophie and Josh. He tempts Josh to join him while using
necromancy to raise thousands of corpses to assault the Elders, Flamel, and Sophie. Josh almost agrees, but at the last moment, he realizes he will lose Sophie if he agrees. Dee brings all the dead in a nearby cemetery alive and they start to attack them, Josh hits Dee with their
Hummer, distracting Dee long enough to escape with Scathach, Sophie and Nicholas Flamel by using a (a
teleportation device where two or more lines of energy,
ley lines, cross each other) to go to Paris which is Nicholas Flamel's old home. The book ends when Dee surprises them. ==Special editions and cover variations==