An experimental nuclear research centre in caves under the moors is experiencing mysterious power losses and mental breakdowns of the staff. The Doctor (Jon Pertwee) and Liz (Caroline John) meet up with Brigadier Lethbridge-Stewart (Nicholas Courtney) to investigate. They travel in the Doctor’s bright yellow antique car, Bessie. A worker is found dead with giant claw-marks on his body, and his companion is nearly mad with fear. They find him drawing cave-paintings on the hospital-room wall, and then he tries to throttle the Doctor. The director Doctor Lawrence (Peter Miles) resents the UNIT investigation. Major Baker (Norman Jones) believes there is a saboteur, and the Doctor finds that the logs have been tampered with. When he enters the caves, he is attacked by a dinosaur-like creature, but its attack is called off by a strange whistle.
Major Baker has shot a man-sized creature and the Doctor calls it a higher reptile. The creature goes up to the moors and hides in a barn. Doctor Quinn (Fulton Mackay) goes to a hidden base in the caves and demands the creatures give him the knowledge he was promised. He is told he must help the wounded creature first and is given a signal device that whistles. The creature attacks a farmer and his wife. The former dies of heart-failure, but the wife survives and describes her attacker. Liz is knocked unconscious in the barn and it escapes. The Brigadier and the Doctor follow its tracks, which end at tire-marks on the road. In Quinn’s office, the Doctor finds a globe of the Earth as it was 200 million years ago, and notes about the Silurian Era.
Quinn is found dead. The Doctor takes his signal device and is surprised by the wounded Silurian, which runs away when he tries to communicate with it. Baker is captured by the Silurians. The Doctor and Liz follow his trail and use the signal to open the way into the Silurian base, where they find Baker in a cage. They see a Silurian being revived from hibernation, in the machine that has been draining the reactor’s energy. The Permanent Under-Secretary, Masters (Geoffrey Palmer), arrives, listens to the Doctor suggesting peaceful contact, but refuses. The Doctor tries to warn the Silurians, but they lock him up. One of the Silurians tells the Doctor their race hid underground when they saw the Moon approaching Earth, millions of years ago, but the hibernation mechanism did not awaken them until the nuclear reactor went online. One Silurian infects Baker with bacteria before he is released, but another gives the Doctor some of the bacteria so he can find a cure and is killed for his pains. The Doctor warns everyone in the Centre not to approach Baker, who collapses. Masters decides to return to London, unaware that he is infected. Baker dies in hospital.
The Doctor works on a cure. Masters eludes the search, spreading the infection. The Doctor finds a cure but the Silurians abduct him. Liz discovers his formula, which is quickly mass-produced and distributed. The Silurians seek to use the reactor to destroy Earth’s Van Allen Belt, but the Doctor overloads the reactor. The Silurians return to the caves to wait for the radiation to die down. The Doctor wishes to revive the Silurians and seek a peaceful compromise with the ancient species, but UNIT Destroys their base.
The seven-episode serial was well-received, despite its length, the unfortunate music, and the Silurians rubber suits. There were two sequels—The Sea Devils in 1972 with Pertwee, and Warriors of the Deep, with Peter Davison, the fifth Doctor, in 1984. It was influenced by the Quatermass movies.