Sophie and Josh Newman – 15 year-old twins – are in Paris with the alchemyst, Nicholas Flamel, and his friend, Scathach. They now face Niccolò Machiavelli and his colleague, but also rival, John Dee, who both work for the Dark Elders. Machiavelli is plotting to capture the twins and Flamel with the missing pages of the Codex – or Book of Abraham the Mage – before Dee can arrive in France from San Francisco. The twins seek out a friend and student to Nicholas, Comte de Saint-Germain, who teaches Sophie to use the elemental magic of Fire. Saint-Germain’s wife, Joan of Arc, helps Sophie to learn to control her aura and to sort out the Witch of Endor’s memories from her own. Josh is given the legendary stone sword Clarent, twin blade of Excalibur, by Nicholas. Clarent is an ancient Fire Elemental sword. Josh, Joan, and Scathach encounter three Disir, more commonly referred to as Valkyries. The Disir are ancient enemies of Scathach and bring along the soul-devouring Nidhogg, a ferocious monster once trapped in the roots of Yggdrasil – the world tree. The monster was freed after Dee destroyed Yggdrasil and attacks Scathach but fails to slay her. Instead, it captures Scathach in its claws, but flees with Scathach when the ancient sword Clarent, wielded by Josh, wounds it. Meanwhile, Nicholas’ wife, Perenelle Flamel, who had been captured, is taken to Alcatraz as a prisoner.
While Josh is fighting Nidhogg, Joan of Arc and Sophie are busy fighting two of the Disir. After a lengthy battle, Sophie manages to freeze the two in an iceberg. They chase after Nidhogg. As Nidhogg flees, Dee, Machiavelli and Dagon (Machiavelli’s assistant), who are watching, express remorse at the Disir’s failure. Machiavelli then allows Dagon to chase Nidhogg and kill Scathach if the beast fails to do so. The monster escapes through the streets of Paris, leaving a trail of destruction in its wake. One of the trio of Disir, as well as Josh (who is still trying to save Scathach) follow. They arrive on the banks of the Seine and, with the help of Dee, Josh manages to stall the Disir and escape. He then leaves with Dee and Machiavelli. Sophie, Joan, and Nicholas arrive, defeat the Disir and Nidhogg, but Scathach gets pulled into the water by Dagon. She isn’t seen for the rest of the book.
On Alcatraz, Perenelle is helped by the ghost of Juan Manuel de Ayala, a Spanish sailor. She gets attacked by the Morrigan because Dee has authorized her to be killed. Underground, Perenelle meets Areop-Enap, the spider elder. The elder explains that Dee couldn’t have Areop-Enap killed because other elders would investigate. Together, the two incapacitate the Morrigan and her thousands of crows that accompanied her.
Sophie, Joan, and Nicholas are talking to Scathach when Dagon erupts out of the river and drags her back in with him. The group miss Scathach, but decide to go after Josh, and, by using Sophie’s aura, they track Dee and his comrades to the catacombs of Paris. There, Josh’s magical ability is awakened by Mars Ultor and he is given a special “gift” similar to what Sophie received from the Witch of Endor – Josh now has Mars’ military knowledge. When Sophie, Josh, and the rest escape from the catacombs, Dee and Machiavelli have set a trap, making the gargoyles and statues of Paris come to life and attack. Josh, Sophie, Saint-Germain, and Joan of Arc combine powers to destroy the statues. Flamel and the twins escape via a train and head for London. Perenelle is still stuck on Alcatraz and fears recapture.