The second installment in the Secrets of the Immortal Nicholas Flamel series picks up immediately after
The Alchemyst. Nicholas Flamel, a centuries-old alchemist whose immortality spell depends on the Codex (the Book of Abraham the Mage), is running out of time. His enemy, the immortal English magician Dr. John Dee, has seized the Codex on behalf of the Dark Elders, ancient beings who once ruled Earth and seek to reclaim it. Without the book, Flamel and his wife, the sorceress Perenelle, will die within weeks. Flamel retains the Codex's final two pages, containing the Final Summoning, a spell Dee needs to bring the Dark Elders back. Perenelle is imprisoned on Alcatraz Island, guarded by a sphinx that drains her magical energy.
Flamel has fled to Paris through a leygate, a portal connecting invisible lines of planetary energy. With him are 15-year-old twins Sophie and Josh Newman and Scathach, an ancient warrior known as the Shadow. Sophie's magical abilities have been Awakened by the Elder goddess Hekate, and the Witch of Endor has trained her in Air magic and transferred thousands of years of memories into her mind. Josh remains un-Awakened and increasingly envious of his sister's powers.
In Paris, Niccolò Machiavelli, an immortal who serves the Dark Elders and heads the French secret service, receives orders from Dee to capture the group. Machiavelli traces the ley line to the basilica of Sacré-Coeur, where Flamel has triggered security alarms. He animates a tulpa, a creature shaped from church candle wax, to delay the group. Sophie destroys the tulpa with her blazing aura but exhausts herself. Flamel secretly instructs Sophie using sign language, and she draws on the Witch's memories to summon a thick fog that allows them to escape into Montmartre.
On Alcatraz, Perenelle realizes the sphinx cannot suppress her innate gift for communicating with ghosts. She persuades the ghost of Juan Manuel de Ayala, the 18th-century Spanish sailor who discovered the island, to lure the sphinx away by acting as a poltergeist, giving her powers time to regenerate.
Flamel phones the Witch of Endor, who tells him to wait at the Eiffel Tower for an ally. At a café, Scathach warns the twins that overusing magical power can cause spontaneous human combustion, as magic feeds off the user's flesh once auric energy, the body's reserve of aura power, is depleted. When police spot the group, Scathach defeats them single-handedly. The group splits up, and Josh confronts Flamel, admitting Dee called him a liar who hoards the Codex's power. Flamel insists he and Perenelle are only the Codex's Guardians and that the twins are the figures described in its prophecy. He warns that the Dark Elders view humanity as slaves or food.
At the Eiffel Tower, the Witch's contact arrives: the Comte de Saint-Germain, an immortal rock musician and alchemist who studied under Flamel centuries ago. As Machiavelli's forces close in, Flamel hands Josh the two Codex pages and Saint-Germain creates a diversion by peeling butterfly tattoos from his arms, which fly up the tower and ignite into a fireworks display. The group escapes, though Flamel is briefly captured before freeing himself by transmuting his aura into sugar to attract ants that overwhelm the officers.
Saint-Germain leads the group to his town house, where they meet his wife, Joan of Arc, made immortal centuries ago by a blood transfusion from Scathach. Joan shares Sophie's rare pure silver aura, and this connection allows Joan to speak directly to Sophie's unconscious mind while the girl sleeps, helping her organize the Witch of Endor's overwhelming memories. Saint-Germain then teaches Sophie the Magic of Fire, burning a permanent tattoo onto her wrist that serves as a trigger to activate the power.
Flamel retrieves two objects hidden centuries ago: a parchment map of European ley lines from his tombstone at the Musée de Cluny, and Clarent, a short stone sword from the lintel of his 15th-century home. Clarent is the twin of Excalibur, known as the Coward's Blade because the legendary Mordred used it to kill King Arthur. Flamel insists Josh carry it, and Scathach reluctantly agrees to teach Josh basic sword handling.
On Alcatraz, Perenelle escapes her cell and discovers dozens of cells filled with sleeping monsters secured behind silver spiderwebs. She realizes Dee is assembling an army. The webs are too thick for any normal spider, suggesting something far more dangerous lurks in the caves below.
Dee arrives in Paris and joins Machiavelli, who has summoned the Disir, three ancient Valkyrie warriors and Scathach's sworn enemies. The Disir bring Nidhogg, a primeval creature resembling a massive Komodo dragon. At dawn, Nidhogg smashes through Saint-Germain's house. Josh stabs it with Clarent, hardening its flesh, but the monster seizes Scathach and flees. Sophie combines Fire and Air magic to freeze the two Disir inside the house while Joan duels them. Josh pursues Nidhogg through the streets, driven by Clarent's power.
On the banks of the Seine, Dee saves Josh from the third Disir and tells the dazed boy that Scathach escaped, ushering him into a car with Machiavelli. Josh does not realize Dee is manipulating him. Dagon, Machiavelli's non-human servant and the last of an ancient aquatic race, drags Scathach into the river to avenge her destruction of his people. Joan defeats the third Disir, and Sophie stabs Nidhogg with Clarent, petrifying the creature as it crashes into the Seine.
Sophie tracks Josh's golden aura traces to a manhole leading into the Catacombs of Paris. Underground, Dee leads Josh to a bone chamber where Mars Ultor, the Elder once worshipped as the God of War, lies petrified. Mars reveals he Awakened his twin sons Romulus and Remus, whose heightened emotions led Romulus to kill his brother. Despite this, Mars performs Josh's Awakening after the boy insists, desperate to reclaim the power he briefly felt through Clarent. Mars transfers an additional unnamed gift that causes an explosion of golden energy.
Sophie bursts into the chamber and confronts Mars, using the Witch's memories to reveal his original name and the curse the Witch placed on him. Flamel transmutes the bone floor into liquid, trapping Mars, and the group escapes through a passage into Notre Dame Cathedral. Dee encases Mars in hardened bone and pursues them.
On the cathedral roof, Dee and Machiavelli animate hundreds of gargoyles. Josh, drawing on Mars's gift, realizes that rapid heating followed by rapid cooling will shatter stone. Saint-Germain bathes the gargoyles in fire while Sophie blasts them with arctic wind. When Saint-Germain and Joan collapse, the twins continue together, their combined auras amplifying each other's power until every gargoyle crumbles to dust.
On Alcatraz, Perenelle discovers Dee has imprisoned Areop-Enap, an enormous spider Elder, deep below the prison. The creature is bound by Words of Power, ancient binding spells older than the Elders. Perenelle frees Areop-Enap, who opposes the Dark Elders' return. Together they confront the Morrigan, a Crow Goddess who arrives with a vast flock to kill Perenelle. Areop-Enap's webs ensnare the birds, and Perenelle imprisons the Morrigan.
In the aftermath, Machiavelli reveals he recorded Dee's incriminating statements, forcing an alliance. He proposes they capture the twins, arguing that whoever controls them controls the world. Flamel, Sophie, and Josh board the Eurostar using false passports, heading to London to find Gilgamesh the King, the oldest immortal human, who can train the twins in the Magic of Water. As the train departs, the Genii Cucullati, hooded flesh-eating creatures sent by Dee, follow them, confirming the danger has pursued them to England.