Alithea Binnie is a British narratology scholar who occasionally hallucinates demonic beings. During a trip to Istanbul, Alithea purchases an antique bottle and unleashes the Djinn trapped within it. The Djinn offers to grant Alithea three wishes, so long as each one is truly her heart's desire. However, Alithea argues that wishing is a mistake, accusing the Djinn of being a trickster. She says that when she was a child, she created an imaginary friend in the form of a young boy and even imagined his whole life (which she wrote in a diary) but decided to forget about him, fearing to be overwhelmed by her own imagination. In response, the Djinn proceeds to tell her three tales of his past and how he ended up trapped in the bottle.
In the first story, the Queen of Sheba, the Djinn's cousin and lover, is wooed by King Solomon, who imprisons the Djinn in a bottle which is cast into the Red Sea by a bird. The second story centers on Gülten, a concubine in the palace of Suleiman the Magnificent. After finding the bottle, Gülten wishes for Suleiman's son, Mustafa, to fall in love with her and subsequently wishes to bear his child. Hürrem Sultan, a favored concubine of Suleiman, schemes to have her own son on the throne and convinces Suleiman that Mustafa is conspiring against him; this results in Mustafa's murder. Despite the Djinn's attempts to save her, the pregnant Gülten is also killed on Suleiman's orders as she refuses to make her final wish, or at least desists from timely doing so.
The Djinn wanders the palace for over 100 years, invisible due to the concealment of the bottle. He almost captures the attention of Murad IV, who goes to war and becomes a ruthless ruler, later dying from alcoholism. His brother Ibrahim becomes the new sultan and develops a fetish for fat concubines. His favorite among them, Sugar Lump, uncovers the bottle after slipping. The Djinn appears to her and desperately begs her to make the third wish. Thinking he is a trickster, Sugar Lump wishes for the Djinn to be re-imprisoned in his bottle at the bottom of the Bosporus.
In the final story, Zefir, the slave of a Turkish merchant, is given the bottle after it is recovered in the mid-19th century from the belly of a gutted fish. Zefir wishes first for all-reaching knowledge, which the Djinn grants in the form of books, and later to perceive the world as djinns do. Despite the Djinn's growing affection for Zefir and the fact she is now pregnant with his child, she grows increasingly crowded by his unwillingness to let her make a third wish and end their bond. The Djinn offers to reside in his bottle whenever she wishes. However, Zefir wishes to forget she met the Djinn, leaving him imprisoned and unknown once again. This last story moves Alithea to the point where she wishes for the Djinn and herself to fall in love, resulting in them having sex.
Afterwards, the Djinn and Alithea decide to travel back to London.
One day, Alithea discovers that the Djinn is becoming weaker due to the effects that the city's cell tower and satellite transmissions have when interacting with his electromagnetic physiology. She uses her second wish to get the severely ill Djinn to speak again, apologizes for using her wish to deny them the chance to fall in love naturally, and uses her third and final wish to set the Djinn free, so he is able to return to "The Realm of Djinn".
Three years later, Alithea has written a book containing all the stories that the Djinn told her, like she once did with her childhood imaginary friend. Though expecting never to see him again, the now-healthy Djinn visits Alithea three years later and periodically returns throughout her lifetime.
