After receiving honorable discharges from the British Army in Palestine in 1918, Professor Holly (Peter Cushing), young Leo Vincey (John Richardson) and their orderly Job (Bernard Cribbins) embark on an expedition into a previously unexplored region of north-east Africa. They discover the lost city of Kuma after Leo receives a mysterious map revealing the city's whereabouts.
This lost realm is ruled by Ayesha (Ursula Andress), who is also known as "She-Who-Waits" and "She-Who-Must-Be-Obeyed." Ayesha is an immortal queen and high priestess who believes Leo is the reincarnation of her former lover, the priest Kallikrates (whom she killed when she found him in an intimate embrace with another woman about two thousand years before). Ayesha tries to convince Leo to walk into a ceremonial fire after it has turned blue, which happens once certain astronomical events coincide. These conditions are met for only a short period and only occur rarely. By entering the fire, Leo himself will become immortal.
As this is happening, Ayesha's army is attacked by her enslaved tribesmen, the Amahagger. Although Ayesha had oppressed the Amahagger for 2,000 years, the uprising was triggered by the queen's executing Ustane (Rosenda Monteros), an Amahagger woman who had developed a relationship with Leo, in a fit of jealousy.
Ustane's father, Haumeid (André Morell), who like his daughter had befriended Leo, Holly and Job, is outraged at his daughter's execution and incites the Amahagger into the uprising. Ayesha's army is overwhelmed during the fierce battle against the poorly equipped yet numerous Amahagger.
Whilst the uprising is taking place, Leo battles Billali (Christopher Lee), Ayesha's fanatical priest, who wants immortality for himself, believing it is his due after his years of selfless service. After dueling with Leo and finally gaining the upper hand, Billali, giving Leo up for dead, attempts to enter the blue flames himself and become immortal but is killed by Ayesha before he can enter the fire.
Ayesha takes Leo's hand and leads him into the fire. Upon entering, Leo becomes immortal, but Ayesha's second exposure to the fire destroys her immortality and she dies almost instantly as the centuries catch up with her and her ages millennia in a few seconds. The film ends with a despondent Leo stating that he doesn't care when the fire will next burn blue but it will find him waiting for it.
