Enchantress picks up where its predecessor, The Warlock, left off. Two of its central characters, the fifteen-year-old twins, Sophie and Josh Newman, have been re-united after being briefly separated. The twins, along with John Dee and Virginia Dare, go back in time to the Isle of Danu Talis, where Osiris and Isis are revealed to be Dee’s masters and the twins’ parents. Osiris removes Dee’s immortality, but Dee does not immediately die (he is later found by Marethyu, who restores his health and sight). Virginia Dare chooses to side with Osiris and Isis.
Meanwhile, the Flamels, Niten, and Prometheus discover that Mars, Hel, and Odin are not faring well and that Machiavelli and Billy the Kid have joined them. After successfully turning the monsters on each other, the Flamels join them on Alcatraz. But Billy mistakenly throws the spear heads with the Words of Power at Perenelle (he also used them to kill the Sphinx earlier). The Morrigan throws herself in front of Perenelle and dies instead. Odin and Hel both die slaying an army of Anpu. After finding Aerop-Enap’s cocoon, the Flamels and Machiavelli attempt to awake her while Billy and Black Hawk fight a Karkinos (giant crab). Billy is mortally wounded and Black Hawk is thrown into the water, presumably eaten by the Nereids. Machiavelli heals Billy and Aerop-Enap kills the Karkinos. Tsagaglalal returns herself to her youthful immortal state and it is discovered that she is one of the First People that were awakened by Prometheus. After putting on an ancient suit of ceramic armour, she goes to the Golden Gate Bridge to fend off an army of Spartoi that were animated by Quetzalcoatl and Bastet. Vowing to keep them from entering the city, Niten and Prometheus defeat quite a few of the Spartoi, but both are killed. After slaying the rest of the Spartoi, Tsagaglalal finds them, but only has enough of her aura left to heal Prometheus. The Elder convinces her to use her aura to heal Niten, asking her to tell him to marry Aoife, whom Niten loves. Quetzalcoatl and Bastet flee after they hear Tsagaglalal roar out of rage.
On Danu Talis, Scathach, Joan of Arc, Saint-Germain, Palamedes, Shakespeare, and the young Prometheus crash their vimana on the original Yggdrasill and meet Hekate and Mars (then Huitzilopochtli), who plan to lead the human inhabitants of the Yggdrasill to liberate the incarcerated Aten. Anubis and his mother Bastet prepare to take over Danu Talis by making Anubis ruler, but Isis and Osiris have other plans. Telling Sophie and Josh to put on silver and gold suits of armour, they prepare to present the twins to the council of elders as the rightful rulers of Danu Talis. Marethyu presents Dare and Dee with tablets each containing personal messages, and Dare’s convinces her to side with the humani. Marethyu then proceeds to watch Josh and Sophie enter the pyramid because he knows that it will be the last time they get to laugh with one another. While Josh and Sophie wait to be presented, they are attacked by berserkers (bear hybrids), and Tsagaglalal (She Who Watches) comes to the rescue. Dare meets Dee in front of the prison, later telling him that she had only wanted a world so that she could make it completely free. She leads the humani against the Elders along with Dee, who dies when allowing her to draw energy off of his aura so she can save the humans from the warden’s counter-attack.
Scathach, Joan, Saint Germain, Shakespeare, and Palamedes fight the final battle along with the twins. Osiris and Isis admit that Sophie and Josh aren’t their children (Josh was found in a Neanderthal camp shortly after the Fall of Danu Talis, and Sophie was found in Russia in the ninth or tenth century 30,000 years after) and they transform into their true forms, revealing that they aren’t Elders, but Earthlords. After defeating the pair, Tsagaglalal presents them with tablets from Abraham The Mage. Completing the prophecy “twins with the auras of silver and gold, a brother and sister with the power to either save the world … or destroy it.”, Sophie leaves Josh to destroy Danu Talis. Josh sits on the center of the Pyramid of the Sun and begins to read the Codex, discovering that Sophie, Joan, Scathach, Dare, and Aten lead the survivors onto the new Earth and assist them for several hundred years before returning to the present time. He then combines the Four Swords of Power (Clarent, Excalibur, Durendal, and Joyeuse) to create the fifth power— Aether. The swords forms a hook, revealing that Josh becomes/is Marethyu (hence the reason characters have always thought Marethyu seemed familiar). He plunges his hook into the center of the Pyramid of the Sun, speaking aloud the last words he read in the Codex (“Today I become Death, the destroyer of worlds”) and there by destroying Danu Talis. On Alcatraz, Nicholas and Perenelle spend their last moments together, content. Marethyu appears and tells Perenelle and the Alchemyst that he is Josh and takes them to Paris, apparently for the Flamels to die. But in a letter to Sophie, Josh (Marethyu) reveals that he and the Flamels were present at Aoife and Niten’s wedding, where Scathach was the bridesmaid. And they live happily ever after, with Earth saved.