The main story arc charts the adventures of fifteen year old twins Sophie and Josh Newman, whose regular lives working at their summer jobs (Sophie works in a coffee shop, Josh works in a bookstore) are turned upside down by the arrival of Dr. John Dee. Dr. Dee engages the bookstore owner Nick Fleming in a battle of magic in an attempt to steal an ancient book, The Book of Abraham the Mage (aka the Codex) from him. Dr. Dee snatches the book from Josh’s grasp but Josh manages to retain two pages. Dr Dee also kidnaps Nick’s wife Perry in the melee and imprisons her on Alcatraz Island.
After the battle Nick Fleming confesses to Josh and Sophie that his real name is Nicholas Flamel, that he is the French alchemist from history, that he is also immortal, and that the twins, himself and Perry (his immortal wife, Perenelle Flamel) are in grave danger. Nicholas tells the twins that he believes them to be mentioned in a prophecy within the Codex, and that the fate of the world as they know it could depend on his success in getting their latent magic awakened. He also tells them that without the Codex, both he and Perry will die within a month, as their immortality depends on a recipe for a special elixir found only within its pages.
Meanwhile Dr. Dee has found out that he is missing two very vital pages from the Codex. The pages are the Final Summoning, needed by him to return his masters, the Dark Elders, to the face of the earth … and so begins a fast paced race as Dee pursues the twins, Nicholas for the pages of the Codex, whilst Nicholas aided by Scathach and others race to get the twins’ latent magical auras awakened, to get them schooled in the use of the elemental magics, and to rescue his beloved Perry.
The stories criss-cross the globe featuring well known places and sites, such as San Francisco, London, the Eiffel Tower, Stonehenge and the Golden Gate Bridge. Many characters from history and mythology help both sides pursue their goals. In the first four books alone, Scathach, Hekate, Prometheus, the Witch of Endor, Gilgamesh, Niccolò Machiavelli, Bastet, Odin, William Shakespeare, Joan of Arc and Mars Ultor were just some of the characters that had entered this series.