The planet Karn is home both to a mystic Sisterhood, whose sacred flame produces an elixir of life, and to Mehendri Solon, a fanatical scientist who is using the remnants of spaceship crash victims to put together a new body for the still-living brain of the executed Time Lord criminal Morbius.

When the Doctor and Sarah arrive on the planet, Solon decides that the Doctor's head is just what he needs to complete his work. The Sisterhood meanwhile fear that the Doctor has been sent by the Time Lords to steal the last drops of elixir produced by the dying flame. They kidnap him and plan to burn him at the stake but he is rescued by Sarah, who is temporarily blinded in the process.

The Doctor is tricked by Solon into believing that his companion's condition is permanent. He asks the Sisterhood for help and restores their sacred flame to its former glory using a firework to clear its blocked chimney. Returning to Solon's citadel, the Doctor and Sarah become trapped in the cellar.

The Doctor releases cyanide fumes into the ventilation system and Solon is killed, but not before he has used an artificial brain case to complete Morbius's new body. The now-mobile Morbius accepts the Doctor's challenge to a mind-bending contest, which takes a heavy toll on both of them. The Sisters force the crazed Morbius over a cliff and he falls to his death. They then use the elixir to heal the Doctor.