On the planet Karn, an insect-like alien crawls away from an escape pod. It is ambushed and killed by Condo, a large man with a hook for a hand, who takes its head to a castle and his master Solon. However, the head is unsuitable — Solon needs a head from a warm-blooded humanoid.
The TARDIS materializes in the middle of a lightning storm, and the Fourth Doctor rushes out, ranting at the Time Lords for diverting him to this planet. Sarah suggests that perhaps the TARDIS malfunctioned again, but the Doctor is insistent there is something going on which the Time Lords do not want to sully their hands with.
The Doctor knows of Solon, who was an authority on microsurgical techniques and tissue transplants. He remarks that Solon’s disappearance caused quite a stir and there were rumours that he had joined the Cult of Morbius. The Doctor now recognises the clay head — it is that of Morbius, one of the most despicably criminal minded Time Lords in history. Before he can say anything further, the drugged wine takes its effect, and the Doctor falls over unconscious. Seeing this, Sarah, who didn’t drink the wine realises it has been spiked and pretends to succumb.
Back at the castle, Condo is angered by Solon’s offer to sacrifice him, and threatens to kill Solon. Pleading for his life, Solon offers to restore Condo’s arm and tells him to prepare the laboratory. Meanwhile, Sarah and the Doctor have escaped the shrine, but Sarah has been blinded by the energy from Maren’s ring. She is worried that it may be permanent, but the Doctor assures her that the flash merely numbed the optic nerves and she should recover in a few hours. Despite Sarah telling him about the headless body she saw, the Doctor leads them back towards Solon’s castle.
Solon summons Condo, who leaves Sarah in the parlour. Solon gives a note for Condo to pass to the Sisterhood before the Doctor gets there. Sarah hears Morbius’s voice calling for Solon. Following the sound, she enters a hidden laboratory. As she stumbles blindly towards Morbius, who is a glowing brain in a tank, he accuses her of being a part of the Sisterhood, sent here to destroy him…
Solon enters and drags Sarah out of the laboratory. As he closes the door, Sarah hears Solon address the voice as “Morbius” and hears how Solon has sent the Doctor into a trap. Sarah locks Solon in the laboratory and, still blind, makes her way out of the castle.
Maren still does not believe — she saw Morbius being dispersed. The Doctor asks if Solon was here at that time, and Maren says many came to Karn at the time. Morbius led an army of mercenaries, promising them the Elixir and immortality and revealing its existence to the cosmos. The Doctor tells Maren that if she wants his help, the wrecking of spaceships simply passing by Karn has to stop. Outside, Sarah continues to work her way along the rocks and runs into Condo, who had orders to find her. He tells her the Doctor is dead and carries her, struggling, back to the castle.
Ohica starts to thank the Doctor, but he stops her, saying that Sarah and he have another engagement. Before they leave, he gives her a pair of curious objects in case they need to relight the Flame again. When Ohica asks what they are, the Doctor answers, “A mighty atom and a thunderflash.” He explains that the writing on the cardboard tubes reads: “Light the blue touch paper and stand clear.” This time, the TARDIS vanishes in a puff of light and smoke…