Dr. Helen Smith becomes concerned over the mental state of one of the pilots, Harry Sanders. She expresses her concerns to the base's second in command, Michael Lebrun, and tries to convince him to get Commander Ransom to remove the pilot from duty. Ransom refuses and assigns Sanders to pilot the Commander's shuttle for a trip to Earth. After an malfunction, Sanders cuts the communications link and goes outside the shuttle to make repairs and is thrown into space. When Ransom attempts to pilot the shuttle it explodes. The European agency sends a Welch scientist to take over the station and to investigate the shuttle accident.
After a number of mysterious deaths, paranoia sets in as the crew begins to believe the deaths are being committed by a ""Moon Monster"" living on the surface of the Moon.
The station's crew suffers from an unusual number of accidents and mistakes. Director Caulder must deal with the problems while trying to operate within his Earth-bound superiors' budgetary limitations.
An auditor is sent to Moonbase 3 from the European Headquarters in Brussels to investigate whether or not the cost of operating the base is justified. Director Caulder demands results for the base scientists as Dr. Helen Smith becomes concerned over the stress on the staff, especially Steven Partness.
An accident strands Tom Hill in a shuttle between Earth and the Moon. The only person who can save him is Colonel Gararov, a Russian cosmonaut. However, to rescue Hill, Gararov would have to disobey the orders of his superior: General Trenkin, Commander of the Russian moon base.
The Artic Sun Project proposes to use a nuclear explosion over the Artic, thereby, melting the ice and creating a ""Garden of Eden."" The project's designer, Sir Benjamin Dyce comes to Moonbase 3 in an attempt to stop the program for fear that the explosion can not be contained and it will lead to the extinction of mankind. Dyce is unable to convince others of his concern and the nuclear device is detonated. As a thick haze covers the Earth, the Moonbase scientists worry Dr. Dyce may be right.
