Summoned by the Brigadier to an underground research centre at Wenley Moor, the Doctor and Liz Shaw learn from its director, Dr Lawrence, that work on a new type of nuclear reactor is being hampered by inexplicable power losses and by an unusually high incidence of stress-related illness amongst staff.

Investigating a nearby cave system, the Doctor discovers it is the base of a group of intelligent reptiles, termed Silurians, who went into hibernation millions of years ago but have now been revived by power from the research centre.

The Doctor strives for peace between reptiles and humans and manages to gain the trust of the old Silurian leader, but then a rebellious young Silurian seizes power and releases a deadly virus that threatens to wipe out humanity.

The Doctor finds an antidote, but the Silurians retaliate by taking over the research centre and preparing to destroy the Van Allen Belt, a natural barrier shielding the Earth from solar radiation harmful to humans but beneficial to reptiles. The creatures are tricked into returning to their caves when the Doctor overloads the reactor, threatening to cause a nuclear explosion. The Brigadier, to the Time Lord's disgust, then has the Silurian base blown up.