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A strange man who goes by Dr John Dee shows up at a book store owned by Nick Flemming. Josh comes out of the cellar while working at the shop to find the store in tatters, while Dr Dee and Mr Flemming are hurling strange bombs at each other. Dr John Dee steals a book, and walks away leaving the book store in tatters. This is when Sophie, Josh's twin, shows up with Mr Flemming's wife, Perry. Sophie also has no idea what's going on. But not before Josh can steal some pages out of the book.

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Nick Flemming, who has reintroduced himself as Nicholas Flamel, the Alchemyst who discovered the secret to eternal life, takes the twins, who are confused and in great danger, to an alley crawling with rats. They enter a suspicious looking door, and almost fall victim to booby traps. Then, Nicholas leads them into a side door, where a strange young woman with bright red hair, standing in a completely white dojo, wearing a white robe. He introduces her as Scathach, "the Warrior Maid, the Shadow, the Daemon Slayer, The King Maker. "She introduces herself as Scatty

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After narrowly escaping death at the hands of the Morrigan, a Next Generation elder who is the Goddess of death and crows, Josh, under Nicholas Flamel's instruction, drives them to a mysterious road in Mill Valley, CA. They are greeted by mysterious boar, which are introduced as Torc Allta, or wereboars. They drive through a mysterious curtain of vines, and behind it stands a beautiful woman, with black, stone-like skin, and butter-colored eyes. Flamel says that her name is Hekate, one of the Elders, Goddess of Magic. Hekate is interested in the twins, and the prophecy that they just might fulfill. She shows them their auras, which are silver and gold, the rarest colors. Then, she lead them to her home, Yggdrasill, or The World Tree of Norse Mythology.

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Sophie comes over to Josh's room in the Yggdrasill. They recap on everything that they've learned, and try to make sense of everything and come up with a plan. That plan is to run away at night. Scathach puts them to bed, then runs off somewhere in the tree. Then, they escape. They head through the tree, across the field, and to the car, all while listening to the creepy noises around them. They get in the ca, and it won't turn on. The realize that all sources of power (AKA Electronics) have been drained by the Yggdrasill. Then, the weird, ugly, bird monster appears, and starts walking towards the car. The twins have locked themselves inside. Then, two more appear. They hop on the hood of the car, and the twins start freaking out. Then, it talks, and says that it is not there enemy. It takes them back to the tree, where Scatty is waiting.

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Dr Dee and the Morrigan recruit Bastet, one of the elders and the goddess of cats, and then begin to invade Hekate's shadowrealm with their army of birds and cats. While all of this is going on, Hekate and the twins have been led deep below the Yggdrasil, where Hekate has agreed to awaken their magical powers. Nicholas Flamel and Scathach are fighting off the soldiers. Sophie is awakened first, and she is out in a state of extreme pain. Her senses are super heightened, and she passes out because it's so overwhelming. Then, Hekate runs out to the battle, because they have set fire to the tree. Josh grabs Sophie, and Nicholas leads them out through the roots, and picks up Scatty along the way. They make a dash out to the battlefield, and Sophie, who gets briefly possessed by Perenelle, who is currently in the basement of John Dee's company, and scares off Bastet. They make a mad dash, and leave the Shadowrealm. John Dee shoves Excalibur, the sword of ice, into the tree, killing Hekate and destroying the shadowrealm.

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Perenelle wakes after she gives her warning to Nicholas about Bastet on a cold, damp floor. She realizes that she is trapped on Alcatraz. She knows that her aura will strengthen again, and she will be able to get out soon. Then, she hears claws on the stone, and a sphinx shows up in front of the bars. Perenelle realizes that she is trapped here, as spinxes naturally absorb auric energy. She then starts to think.

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After narrowly escaping Hekate's shadowrealm, the group has headed to Ojai, so Sophie can be trained in the element of air by The Witch of Endor. They enter her shop, and finds she is not their. They are surrounded by mirrors. Nicholas leaves briefly, looking for the Witch. Scathach decides to help Sophie, and releave her of the overwhelming emotions she is feeling. She grabs her hand, and starts talking about the history of the Elders, and their island, Danu Talis, or Atlantis. She explains how after the fall of Danu Talis, the Next Generation of Elders was, strange. Some were born half animal, half human, or an even stranger mix of the two. Some, were born without the ability to feel pain or emotion. These are the ones we call vampires. Some drink blood, some, like Scathach, absorb emotion, which is what she is doing to Sophie, absorbing her pain and fear. When Josh asks why vampires would absorb the emotions, Scatty responds with "So they can feel alove."

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Nicholas Flamel returns with The Witch of Endor, an elderly woman at first sight, who asks to be called Dora. She gives Scathach, her granddaughter, a hug and complains about how she doesn't talk to her anymore. Then, she reveals how she sacrificed her sight to be able to see the future, and now she can only see things through their reflection. Josh and Sophie ask why she couldn't have warned Heakte about what would happen, and she explains that it was one possible future. Then, she ask Josh to leave so she can give Sophie her magic. Sophie is wrapped up in a cocoon of white energy, and absorbs everything the Witch has ever known or seen. Then, they smell sulfur, the scent of Dee's magic, and know something is wrong.

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Sophie, Nicholas, and Scathach head out into the street, which is now covered in fog. Sophie creates a gust of wind with her new magic, and blows some of the fog away, to reveal mummies and skeletons. Nicholas, Scathach and Sophie then begin to fight back, all while Dr Dee is taunting them, saying he will stop the endless horde if they give him the last pages of the codex. Josh wakes up from the strange slumber Dee put him in, and runs and gets the car. Sophie has completely drained her energy, and can't use any magic anymore. Nicholas is in a similar place, and Scathach is still fighting hard. Josh rams the car into the fountain, and Dee accidentally ends the spell. Then, the undead animals start waking up.

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Dora calls the twins, Nicholas, and Scathach into the shop, and leads them to the back. She shows them a strange, fogged up mirror in a closet. She says that this is a leygate, which can be used to travel to other leygates. They activate it, and Nicholas, Scathach, and Sophie jump through. Josh is about to jump through when Dee shows up. He tells him that his sister doesn't really care for him, and tries to convince Josh to come with him. Then Sophie comes back for him, which causes Josh to snap out of it, and they leap through. Dora then knocks the mirror over, and the shop blows up.