The planet Merak II is suffering from a devastating botanical plague. The only thing that can halt the spread of the plague is a substance called zenite and the Enterprise is despatched to the planet of Ardana, which is the only known source in the galaxy of the rare mineral. Kirk and Spock beam down to the planet to collect a consignment of the substance and are unexpectedly attacked by a group of Troglyte miners who are led by a young female.

The miners break off their attack and disappear when two sentinels materialise, accompanying the planet's High Advisor, Plasus. He apologises for the incident and invites Kirk and Spock to visit their cloud city of Stratos until the culprits can be apprehended and a new consignment of zenite prepared. Spock examines the culture of the city in the clouds and notes that the luxurious surroundings of the inhabitants are enjoyed at the expense of the harsh conditions and deprivation endured by the Troglyte miners.

The Vulcan officer is shown around the city by the beautiful, young daughter of Plasus, called Droxine, who is intrigued by him and he becomes noticeably disturbed when she enquires whether anything can affect the seven-year Vulcan mating cycle. Spock is called back by Kirk when the woman who led the miners' attack, Vana, appears in his room. She is taken away by sentinels and tortured for information about the rebellious miners.

When Kirk and Spock discover what is being done to her they try to intervene but are ordered to leave by Plasus. McCoy advises that the zenite which they mine apparently gives off an invisible gas which is the cause of the Troglytes being retarded and violent, but says this can easily be prevented by the use of filter masks. Kirk relays the information to Plasus who dismisses the suggestion with contempt. Kirk rescues Vana and explains about the gas, offering a supply of the filter masks in exchange for their zenite, but she does not believe him and he is taken prisoner.

Kirk manages to overpower her and block the entrance to the mines. To prove to her that what he has been telling her is true he contacts the Enterprise and arranges for Plasus to be beamed down into the mines. The gas slowly takes effect on the pair of them and they begin to fight. Vana uses Kirk's communicator to have them all beamed back to the Enterprise and they soon recover. Now convinced, Vana agrees to provide Kirk with the much-needed zenite in exchange for the filter masks in the hope that, one day, all of her people will be able to live in cloud cities.