The story unfolds around a mysterious crisis at a nuclear-powered cyclotron facility hidden within caves beneath a remote moorland. The facility is experiencing unexplained power drains and a series of mental breakdowns among its staff, prompting urgent investigation by the Third Doctor and Liz Shaw. They are accompanied by the formidable Brigadier Lethbridge-Stewart, who is determined to get to the bottom of these eerie disturbances. The security chief, Major Baker, suspects that a saboteur is within the center, adding an element of suspicion and tension.
During their investigation, the Doctor and Liz uncover a hidden Silurian base deep beneath the caves. Here, they witness a startling scene: a Silurian being being revived from hibernation through a specialized machine. This discovery begins to shed light on the strange energy problems plaguing the reactor, as it becomes clear that these prehistoric creatures are quietly emerging from their ancient slumber.
As the story unfolds, Masters, the Permanent Under-Secretary overseeing the center, arrives on the scene. The Doctor explains his theory that the Silurians—an ancient, reptilian species—are responsible for the disturbances, and he advocates for peaceful contact with them. His plea for coexistence is met with hostility, especially after a tragic revelation: Quinn’s assistant, who was held captive by the Silurian, was murdered by one of the creatures, deepening the distrust between humans and Silurians.
The situation escalates when the Silurians capture the Doctor in a cage, intending to prevent him from interfering. Nevertheless, the Doctor manages to reason with the Silurian leader, who tries to persuade his people to live peacefully alongside humans. Unfortunately, the younger Silurian disagrees and ultimately kills the leader, declaring himself the new authority, which sparks further conflict and tension.
Trouble intensifies as the Silurians, in their quest for survival, infect Major Baker with a deadly strain of bacteria, unleashing an epidemic that threatens to spread across Britain. The Doctor, displaying his quick thinking, works tirelessly to find a cure, which is then mass-produced to contain the outbreak.
However, the danger is far from over. The Silurians capture the Doctor, Liz, and the Brigadier, transporting them to the power plant. There, the Doctor overloads the reactor, knowing it will cause the caves—and the Silurian civilization within—to become radioactively contaminated for at least 25 years. The younger Silurian, willing to sacrifice himself, remains awake to operate the faulty mechanism, which ensures the safety of his species but at the cost of his life. The Doctor and Liz work together to repair the reactor, but recognizing that the younger Silurian has been manipulated, he attacks the Doctor in a desperate act. The Brigadier intervenes by shooting the Silurian to prevent further conflict.
In the final moments, the Doctor emphasizes the importance of allowing the Silurians to hibernate peacefully, advocating for the caves to be left untouched so that future peaceful relations might occur. However, the Brigadier orders the destruction of the caves, effectively killing the Silurians inside. The Doctor is deeply horrified and distressed by this decision, as he had hoped for coexistence and understanding. The story concludes on a somber note, emphasizing the tragic loss of an ancient species and the complex moral questions surrounding disaster, diplomacy, and the cost of survival.
