SPOILER ALERT -- if you haven't read book 1, you may not want to read on, because knowing what happens in book 2 will kind of spoil reading the first one, if you ask me.
This book is named for the evil Dr. John Dee (aka The Magician) as he continues to track the kids and Nicholas, trying to capture his nemesis and secure the last two pages of the Codex. The fact that he has the Codex of course means that Nicholas and Perenell have lost their ticket to immortality and are aging -- which lends a critical time element. Even worse, Dee has captured Perenell and holds her prisoner on Alcatraz, where she has only the ghosts to help her.
The story introduces some interesting new characters: Nicollo Machiavelli (who works for the Dark Elders), the Comte de Saint-Germain (Flamel's former student who can teach Sophie the second elemental magic of fire), and his wife who is a character so great I won't tell you because it will ruin it.
Will Josh have his own powers awakened? Will we finally find out who Dr. John Dee serves? Will Perenell escape from her island prison? You'll have to read The Magician to find out.
Sidenote: The Sorceress, the third book in the series, is slated for release in May of 2009.