What's up with the ending is that it's just the beginning.
Seriously, folks—those are the last words of the book:
"It is ending, Immortal."
"On the contrary […] It is now only just beginning." (41.21-22)
Oh Perenelle, you always know just what to do and say. Even now, when she's imprisoned by magical forces and trapped on Alcatraz by a jerk of a Sphinx, she manages to muster a kick-butt comeback.
See, the thing is, it may be the end of the novel, but Perenelle knows that it's only just the beginning of Sophie and Josh's quest to preserve the Codex and fulfill its prophecy. In many ways, the ending of this book is totally open-ended—anything can happen.
Sophie and Josh, along with their mentors Scatty and Flamel, have jumped through the mirror and are en route to Paris. Perenelle is still trapped in the creepiest prison of all time. Oh, and the Codex? That's still in Dee's hands. And speaking of Dee, just how did he survive that explosion?
If Shmoop's being honest, we have to say we just don't know. So on to The Magician!