In a priory near the village of Fetchborough, four scientists, Adam Colby, Max Steal, Thea Randsom and Dr. Fendahlman, are doing tests on a human skull they found in Kenya, apparently twelve million years old. When Dr. Fendahlman starts using a sonic time scan, trying to get a image of the owner of the skull, the skull itself seems to react, locking onto Thea and releasing something in the priory grounds that kills a passing hiker, who eventually totally disintegrates.
The scan catches the attention of the Doctor and Leela when they are pulled down to Earth by it. The Doctor and Leela set off to find it before it creates a continuum implosion and destroys the planet. They separate and Leela finds the cottage of Mr. Tyler, a local, modern day witch gifted with psychic powers. The Doctor ends up narrowly avoiding death at the hands of the creature created by the skull, which then kills the leader of a detachment of guards Fendahlman has brought in after the death of the hiker, sealing everyone into the priory.
Mr. Tyler then encounters the creature, but survives and is saved from going into psychic shock by the Doctor, who by this time has worked out that the thing is a Fendahleen, a creature from his planet's mythology, supposedly destroyed when the Fifth Planet broke up. He makes his way into the priory and finds the skull, which tries to kill him. Leela saves him and they go of to the Fifth Planet, only to find that the Time Lords sealed the planet in a Time Loop, making all proper records invisible even to them.
Thea, meanwhile, has been gradually converted into the new core of the Fendahl, a creature that feeds of life energy and leaves nothing behind. Steal, leader of the local black magic cult, recognises this and believes he can control the Fendahl and use it to dominate. He and his followers capture Colby, kill Fendahlman, who was actually influenced through his genetics by the Fendahl to bring this about, and set up the Sonic Time scanner to power the skull and Thea's final transformation.
The Doctor, Leela, Mr. Tyler and her nephew Jack head for the priory only to find the Fendahl core has formed and is converting the cult members into Fendahleen, to form the full circle. The Doctor frees Colby and helps Steal shoot himself after killing one of the new Fendhaleen, in turn fidning out that the Fendahleen are fatally allergic to Salt, leaving the Fendahl core two short of the twelve it needs to be complete and form a gestalt. The Doctor rigs the scanner to implode upon itself and grabs the now dormant skull, leaving with the others only just before the priory is destroyed, along with the Fendalh core and the remaining Fendalheen. The Doctor and Leela then leave and dump the skull near a supernova, thus ending the Fendahl race forever.