A Silurian

While working on his new car, Bessie, The Doctor, is summoned, along with Liz Shaw, by The Brigadier to help him investigate an underground atomic research centre housed in caves below Wenley Moor.

It seems there have been various unexplained problems at the centre which is under the control of its director, Doctor Charles Lawrence. These apparently unrelated problems include a high rate of personnel suffering from stress-related sickness and mysterious power losses which are endangering the research programme of a new type of nuclear reactor. In addition, a scientist, whilst pot-holing in some nearby caves, has been killed with wounds that look like giant claw marks. While his companion, Spencer, has been driven insane. The Doctor and Liz decide to visit Spencer in the sick bay and find that he has been traumatised to such an extent that he can only scrawl primitive cave drawings of reptilian creatures on the walls of his room.

The Doctor is curious as to what happened in the caves and so decides to investigate them himself. He is shocked though when he comes face-to-face with a live dinosaur. He is lucky to escape unscathed when a strange warbling sound seems to call the dinosaur away. The Doctor also finds a human-sized reptilian footprint in the mud. However, when The Doctor returns with The Brigadier and some UNIT troops so as to verify The Doctor's story, the footprint has somehow vanished. When exploring the caves further one of the UNIT troops spots something moving in the shadows and opens fire, apparently hitting something. He is soon joined by the others and they discover a trail of blood leading to where the caves emerge onto the open moor.

The Doctor, Liz and The Brigadier

During the following morning, at a nearby farm, a farmer discovers a strange creature in his barn. When UNIT arrive to investigate they are unaware that the creature is still in the outbuilding. Liz, when she is left alone to take samples, is startled when she sees an upright reptile creature which then flees from the barn.

Unbeknown to The Doctor, UNIT and Doctor Charles Lawrence one of the scientists at the research centre, Doctor John Quinn, discovered the reptile creatures sometime ago. Realising that they are highly intelligent he has been assisting them so that he can gain their scientific knowledge for himself. The Doctor though becomes suspicious of the scientist and so searches his office, at the research centre, and finds a globe of the world as it was 200 million years ago. The Doctor therefore decides to make a visit to see Doctor John Quinn at his cottage. But when he arrives at the cottage he discovers that the scientist has been killed by the creature that had escaped from the barn.

Liz Shaw

Following a map found in Doctor John Quinn's cottage, The Doctor and Liz return to the cave system and discover a base containing a group of the intelligent reptiles, that The Doctor calls Silurians, who went into hibernation millions of years ago. Inside the Silurians’ base The Doctor sees a Silurian being revived from hibernation and realises that this is the reason for the power losses at the research centre.

On returning to the research centre The Doctor learns that The Brigadier plans to enter the caves in force with all his available UNIT troops. The Doctor is alarmed, as he knows that the presence of UNIT troops in the caves will only result in more deaths, and so returns to the Silurians’ base to try and achieve peace between the reptiles and humans. Before The Doctor can stop them the Silurians, on discovering the UNIT troops close to their underground base, trap the soldiers in a cave with no exit. The Doctor though is able to gain the trust of the old Silurian leader – who releases the UNIT troops just before the air runs out.

The Doctor then learns that the Silurians used to be the masters of Earth, long before the humans, but they went into hibernation when it was realised that a small planet threatened to crash into it. The planet though became the Moon and so the disaster predicted by the Silurians never happened, resulting in their extended period of hibernation. Realising that they are the rightful occupiers of Earth and not the humans, and that the Silurians have the ability, and clear intention, to destroy all humans, The Doctor offers to help them live in peace with humanity. The old Silurian leader realises that what The Doctor proposes makes sense and so agrees. But then a rebellious young Silurian seizes power, by killing the old Silurian leader, and releases a deadly virus that threatens to wipe out all of humanity.

Spencer

Soon London is in the grip of the virus, thanks to a government official who returns to the capital after catching the virus during a visit to the research centre. The Doctor eventually finds a cure, but when the Silurians discover this they attack the base and kidnap him. On discovering that The Doctor has disappeared Liz manages to deduce what The Doctor’s cure is and arranges for it to be manufactured and distributed.

This though angers the young Silurian. With his plan thwarted the Silurians decide to retaliate by taking over the research centre and take control of the nuclear reactor with the intention to make the Earth uninhabitable for humans. They plan to use a molecular disperser to convert the research centre's energy to microwaves in order to disperse the Van Allen belt and thus destroy all life on the surface of the planet. In desperation The Doctor is forced into tricking the Silurians into returning to their hibernation units when he overloads the reactor, threatening to cause a huge nuclear explosion.

With the reactor back under control, and the Silurians back in hibernation, The Doctor tells the Brigadier that he proposes to revive the Silurians one-by-one and try again to reach a peaceful compromise between them and humanity. However, The Brigadier has other orders and has the Silurian base blown up, leaving The Doctor horrified and very annoyed with The Brigadier with this act of genocide.