The Brigadier asks the Doctor and Liz to investigate an atomic research station housed in caves below Wenley Moor. There have been various problems at the centre, including personnel going off sick and mysterious power losses which are endangering the research programme under the control of Doctor Charles Lawrence (Peter Miles). In addition, a scientist has been killed whilst pot-holing and his companion, Spencer (John Newman), has been driven insane. The Doctor and Liz visit Spencer in the sick bay and see that he is drawing pictures of monsters on the wall of his room. Suspicious, the Doctor goes into the caves himself and comes face to face with a live dinosaur. He also finds a human-sized reptilian footprint in the mud. When UNIT troops arrive to verify the Doctor's story, the footprint has gone. Major Baker (Norman Jones), the centre's security officer, sees something moving in the shadows and opens fire. He hits something, and the Brigadier, assisted by Captain Hawkins (Paul Darrow), follows the trail of blood to where the caves emerge onto the moor. The creature they have been tracking has, however, taken refuge in a barn and the troops cannot find it. The next morning, the creature attacks the farmer, Squire (Gordon Richardson), whose wife (Nancie Jackson) calls in UNIT. Liz, working alone in the barn, sees the reptile creature as it flees. 

One of the scientists at the centre, Doctor John Quinn (Fulton Mackay), goes into the caves himself. There he enters an alien control centre and is instructed to find and return the wounded creature. To this end he is given a summoning device. Out on the moor, Quinn uses the summoning device to call the creature to him. He hides it in his cottage. Quinn hopes to gain the creatures' scientific knowledge for himself. 

The Doctor is suspicious of Quinn. He searches his office at the centre and finds a globe of the world as it was 200 million years ago. One of Quinn's colleagues, Miss Dawson (Thomasine Heiner), seems to know what is going on, but she will not talk. The Doctor goes to see Quinn at his cottage but he has been killed and the Doctor finds himself face to face with a creature that he calls a Silurian. 

Major Baker returns to the caves and is captured by the Silurians. Following a map found in Quinn's cottage, the Doctor and Liz also enter the Silurians' base. The Doctor sees a Silurian being revived from hibernation and realises the source of the power losses. When he returns to the centre, he finds that Edward Masters (Geoffrey Palmer), the permanent under secretary, has refused the Brigadier's request for more troops to search the caves. Miss Dawson informs everyone that Quinn is dead and the Brigadier determines to search the caves with the men he has. The Doctor re-enters the Silurian base to try and warn them but he is captured. Meanwhile the UNIT troops find themselves trapped in a cave with no exit. 

The Doctor manages to reason with the old Silurian leader (Dave Carter; voice: Peter Halliday). He learns that the Silurians used to be the masters of Earth, but went into hibernation when a small planet threatened to crash into it. The planet became the moon, however, and the disaster predicted by the Silurians never happened, resulting in an extended period of hibernation. The Doctor offers to help them live in peace with humanity. 

Not all the Silurians agree with this suggestion. A young Silurian (Nigel Johns; voice: Peter Halliday) decides to take matters into his own hands, and infects Baker with a virulent disease that the Silurians once used to cull the apes. Baker is released. The old Silurian tells the Doctor what has happened and gives him a sample of the virus so that he might find a cure. When the Doctor leaves, the young Silurian kills the old Silurian, and the virus starts to take hold. First Major Baker, then doctors at the hospital to which he is taken, start to fall ill and die. Liz treats everyone at the base with drugs to ward off the illness, but Masters has already left for London. Soon London is in the grip of the virus, and it spreads to the continent. The Doctor finds a cure, but the Silurians attack the base and kidnap him. Luckily Liz realises what the cure is and arranges for its manufacture and distribution. The Silurians plan to make Earth uninhabitable for humans by using a molecular disperser to convert the centre's energy to microwaves in order to disperse the Van Allen filter belt and thus destroy life on the planet. They return to the base and the Doctor causes a power surge which destroys the disperser unit but which also forces the reactor into overload. The Silurians return to their base where, apart from the young Silurian who must remain to operate the equipment, they return to hibernation. 

The Doctor and Liz manage to stop the reactor and the Doctor returns to the Silurian base. The young Silurian tries to kill the Doctor but the Brigadier shoots it. The Doctor now wants to revive the Silurians one by one in order to reason with them. He also wants to gain their scientific knowledge. He and Liz leave to return to London, but the Brigadier has mined the caves to seal them permanently. The Doctor's car, Bessie, develops a fault and Liz and the Doctor are stuck on the moors as the explosives go off. The Doctor is horrified.

_{Synopsis from Doctor Who: The Third Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos}