The Sorceress is the third installment in the series: The Secrets of the Immortal Nicholas Flamel. In this book, Nicholas Flamel takes the twins (Sophie Newman and Josh Newman (Marethyu) to London, where he uses Francis to enlist Palamedes, the Saracen Knight, and William Shakespeare, to help them. Palamedes takes them to his home, a junk-yard in London, and they manage to work together to contact Perenelle Flamel. Perenelle is trapped on Alcatraz with the friendly but untrustworthy spider elder, Areop-Enap, after narrowly escaping the Sphinx and defeating The Morrigan. The Morrigan had been suppressed sufficiently by the Words of Power that resided on the island that her body was retaken by her two elder sisters, The Macha and The Badb. Perenelle also makes fleeting contact with Scathach and Joan of Arc by Scrying. Areop-Enap and its spider army are then attacked by an onslaught of poisoned flies, killing most of the spiders and wounding Areop-Enap. Meanwhile, Billy the Kid has joined forces with Niccolò Macchiavelli in an attempt to kill the sorceress, but Perenelle, aided by The Macha and The Badb, tricks the pair and steals their boat, traveling back to the mainland.
Unfortunately, the Dark Elders have awakened an ancient being even stronger and more powerful and mysterious than them: an Archon. The Archon, named Cernunnos, is known as the Horned God and is the leader of a pack of wolf people called the Wild Hunt. Cernunnos, the Wild Hunt, and the Magician John Dee engage Shakespear, the Gabriel Hounds (A race of men/wolves), Palamedes, the twins, and Flamel in a vicious battle. Flamel, Palamedes and the twins manage to fight their way past Cernunnos and Dee and flee the destruction of the junkyard. They pick up Gilgamesh the King to teach the twins Water Magic before heading towards Stonehenge, where they intend to take a Leygate back to San Fransisco. What Nicholas Flamel withheld from the twins is that Gilgamesh the King is insane. Though he has no magical aura - and hence cannot use any of his abilities - he can still pass on his knowledge to the awakened human twins. If Gilgamesh refuses to teach the twins, they will have to escape back to San Francisco using the Leygate without this essential knowledge. Thankfully, Gilgamesh agrees to teach the twins the magic of water. While the twins are adjusting to the powers Gilgamesh has taught them, Cernunnos returns with the Wild Hunt and attacks the twins and Gilgamesh. Gilgamesh is wounded by the Archon, but the twins use their newfound magical powers to protect the King. While making their escape, Josh loses Clarent, and Dee grabs the sword, reuniting it with its twin, Excalibur. The two swords fuse together to make a new sword. Flamel, Palamedes and the twins flee for Stonehenge with the Wild Hunt, Dee, and the police after them. They meet up with Shakespeare and the Gabriel Hounds who fled the junk-yard using a secret tunnel, the twins activate the ley lines at Stonehenge and are greeted by Perenelle at the other end.
Meanwhile, Scathach and Joan of Arc try to get to Alcatraz to help Perenelle but are trapped in a Shadowrealm by Machiavelli, who had deliberately set the trap to snare them. They do not know how to return to their time and must try to survive while they wait for Flamel and the others to find and rescue them.