The Magician: The Secrets of the Immortal Nicholas Flamel is the second novel in the Nicholas Flamel series by Michael Scott. In this novel, twins Josh and Sophie find themselves suddenly transported to Paris moments after escaping Dr. John Dee in Ojai, California. Sophie, whose magic has only just been awakened, is exhausted from her efforts in helping them escape first Dr. Dee and later, Niccolo Machiavelli. The twins are finally offered a few minutes to decompress and begin thinking about all that has happened to them. Josh is worried that he cannot trust Flamel while Sophie is all too willing to accept everything that is happening around them. When Dr. Dee and Machiavelli attack again, this time with Valkyries and an ancient monster, it does not seem that it matters which immortal they can trust but whether than can survive creatures that are not even supposed to exist. The Magician is an exciting second installment in the Flamel series that will leave readers begging for more.

Niccolo Machiavelli is called away from an auction just seconds before finally winning the masks he has waited centuries to own. Dr. Dee, a man Machiavelli does not like, but willingly works with because they both serve the Dark Elders, wants Machiavelli to locate Nicholas Flamel and his twin companions and retain them until Dee can arrive in Paris. Machiavelli, who is the head of the Direction Generale de la Securite Etericure, or DGSE, is able to use all his resources to chase after the immortal and his companions. Just as Machiavelli seems to have trapped Flamel, Josh, Sophie, and Scathach outside the Sacre-Coeur Sophie conjures up a fog with spell she recalls from the Witch of Endor's memories.

Flamel knows that they must find a place to rest and regain their strength. Therefore, he has Scathach sit with the twins in a diner while he goes to make a phone call to the Witch of Endor in Ojai. As they wait, Scathach and the twins come under attack by local police officials. Scathach manages to fight them off and get the twins out of the diner safely. They reunite with Flamel who tells them they are to meet a friend under the Eiffel Tower. The four split into groups of two. Sophie goes with Scathach and learns more about Scathach's long history while Josh goes with Flamel and sounds him out about some of the things Dee told him in Ojai.

At the Eiffel Tower, Josh, Sophie, Flamel, and Scathach meet up with the Comte de Saint-Germaine, an old student of Flamel's who is now something of a rock star. Germaine creates a fireworks show over the Eiffel Tower with his fire magic in order to distract Machiavelli and his police force and allow the group to escape. Flamel, however, remains behind to distract Machiavelli's policemen. Flamel is eventually caught, but he uses a spell to change matter into sugar and cause ants to cover the policemen.

At Germain's home, Scathach is thrilled to find Joan of Arc,who has recently married Germain. Joan and Germain welcome Scathach and the twins in their home, giving them food and a safe place to rest. Later, Joan teaches Josh how to use a sword, specifically Clarent, the twin of Excaliber. Germain teaches Sophie how to use fire magic. Just before dawn, while everyone is sleeping, the house is attacked. Josh finds himself coming face to face with an ancient monster called Nidhogg. As Josh and Scathach fight Nidhogg in the kitchen, Joan and Sophie fight two Valkyrie in the living room. Nidhogg takes Scathach and leaves. Josh follows. Josh fights the monster using Clarent, and finds himself filled with a kind of power each time he stabs the creature. As the creature begins to die, Dee catches up to Josh and convinces him to go with Dee and Machiavelli.

Flamel realize what Josh has done and goes after him, but reaches him too late. Nidhogg releases Scathach, but then she is taken into the water by a servant of Machiavelli known as Dagon. Flamel, Joan, Sophie, and Germain go after Josh, finding him the catacombs where his powers have been awakened by Mars Ultor. Mars gives Josh his memories. However, when Flamel and the others come to rescue him, Dee becomes so angry that he kills Mars. Dee and Machiavelli try one last time to take the twins from Flamel because they have finally come to realize that these twins are the twins of legend, but the twins use their powers together as one and defeat them once again.