Horace Holly, a young Cambridge University professor, is visited by Vincey, a colleague who, convinced that he will soon die, charges him with the task of raising his young son, Leo. He gives Holly a locked iron box, with instructions that it is not to be opened until Leo's 25th birthday. Holly agrees. Vincey is found dead the next day, and Holly raises the boy as his own. When the box is opened they discover the ancient "Sherd of Amenartas". Holly, Leo, and their servant, Job, follow instructions on the Sherd and travel to eastern Africa. After surviving a shipwreck, they and their Arab captain, Mahomed, journey into the African interior where they are captured by the savage Amahagger people. The adventurers learn that the natives are ruled by a fearsome white queen who is worshipped as Hiya or "She-who-must-be-obeyed".
Billali, chief of one of the Amahagger tribes, takes charge of the three men, introducing them to the ways of his people. One of the Amahagger maidens, Ustane, takes a liking to Leo and, by kissing him and embracing him publicly, weds him according to Amahagger custom. Leo, likewise, grows very fond of her.
Billali leaves to report the white men's arrival to the queen. In his absence, some of the Amahagger become restless and seize Mahomed, intending to eat him as part of a ritual "hot pot". Holly shoots and kills several of the Amahagger, accidentally killing Mahomed in the process. Leo is gravely wounded in a struggle, and Ustane saves his life by throwing herself onto his prostrate body. Billali returns and declares that the three men are under the queen's protection. Ustane faithfully attends to Leo, but his condition worsens.
The men are taken to the home of the queen near the ruins of the lost city of Kôr, a once mighty civilisation that predated the Egyptians. In a series of catacombs originally built as tombs, Holly is presented to the queen, a white sorceress named Ayesha whose beauty is so great that it enchants any man who beholds it. Ayesha, veiled and behind a partition, warns Holly that the power of her splendour arouses both desire and fear. When she shows herself, Holly is enraptured and prostrates himself before her. Ayesha reveals that she has learned the secret of immortality and that she possesses other supernatural powers including the ability to read the minds of others, as well as healing wounds and curing illness, but she is unable to see into the future. She tells Holly that she has lived in Kôr for more than two millennia, awaiting the reincarnated return of her lover, Kallikrates (whom she had slain in a fit of jealous rage).
The next evening Ayesha visits Leo, intending to heal him. But upon seeing his face she declares him to be the reincarnation of Kallikrates. Ayesha now orders Ustane to leave and never to set eyes on Leo again. When Ustane refuses, Ayesha strikes her dead with magic. Leo becomes bewitched, and despite the murder of their friend neither Holly nor Leo can free themselves from Ayesha's power. Ayesha shows Leo the perfectly preserved body of Kallikrates, which she has kept with her, and then dissolves the remains with a powerful acid, confident that Leo is indeed the reincarnation of her former lover.
Ayesha takes the men to see the Pillar of Fire, passing through the ruins of Kôr into the heart of an ancient volcano. She is determined that Leo should bathe in the fire to become immortal and remain with her forever. Arriving at great cavern, Leo doubts the safety of entering the fire. To allay his fears, Ayesha herself steps into the flame, but with this second immersion her life-preserving power is lost and she begins to wither and revert to her true age. The sight is so shocking that Job dies in fright. Before dying, Ayesha tells Leo, "Forget me not. I shall come again!"
