Dee, joined by his Golem (men of clay) guards, attacks Nick Fleming's (a.k.a. Nicholas Flamel's) bookstore and steals the Codex (minus a few pages).
He also kidnaps Perry, a.k.a. Perenelle. That's Nick's wife.
In his car, Dee places a magical spell on Perenelle so that she is held prisoner.
Everything has gone according to plan, except that he is missing three pages of the book.
He'll have to go back, but first he needs some help.
So he calls the Morrigan, while sending some spies to figure out what Flamel is up to.
By looking through the rat eyes, he realizes Sophie and Josh are twins—perhaps the twins of the prophecy. He decides to destroy them.
Dee imprisons Perenelle in a small windowless room, and he and the Morrigan decide to awaken the Egyptian cat goddess Bastet so that they can attack Hekate and Flamel's crew.
Dee, the Morrigan, and the Bastet send their armies into Hekate's world, the Shadowrealm. Dee enters with his sword, Excalibur, in search of Hekate's home, the World Tree.
Dee plunges his sword into the heart of the World Tree, and the tree spurts a blue stain on everything as it dies. Hekate, whose destiny is linked to the tree, dies too.
Then he howls in rage when he realizes Flamel and the twins have escaped the Shadowrealm in his Hummer.
He learns that Hekate Awakened Sophie's powers, and not Josh's.
The Morrigan, Bastet, and Dr. John Dee decide to bring Josh over to their side and Awaken him. So when they catch up with Flamel's crew in Ojai, Dee tries to recruit Josh, who promptly runs him over with a Hummer. Yeah, that went well.
Dee, bruised, runs into the Witch of Endor's shop just in time to see Flamel, the twins, and Scatty jump through the mirror to Paris. Dee tries one last time to convince Josh to come over to his side, but Sophie steps back through the mirror and they jump to Paris together.
The Witch of Endor shatters the mirror. She tells Dee that he has about 3 seconds to leave the shop, but he doesn't quite make it out before it explodes.