The Enterprise goes to Ardana to obtain the only known cure to a plague that threatens to decimate the vegetation on the planet Merak II. Kirk and Spock go to the cloud city of Stratos, and find out that the population is split between the Troglytes, who do the dirty work, including the mining, and the people of the city who enjoy good lives on the backs of the Troglytes. When the Troglytes rebel and threaten to stop mining, Kirk must solve the civil war to get the plague cure.

In the 21st century, all travel is conducted via T-Mat, an instantaneous travel and transport system operated from a Moonbase. Space flight has been all but forgotten - and as a result, when contact is lost with the Moonbase, there appears to be no way to repair T-Mat system. As the world begins to slide into chaos and anarchy, the Doctor and his companions arrive just in time to volunteer for an emergency rocket flight to the Moon, where they discover that the Moonbase has been invaded by Ice Warriors. Now T-Mat is under their control, and despite resistance from the Moonbase crew, the Ice Warriors will soon be able to use it as a weapon to transmat deadly seed pods to Earth, transforming the planet's atmosphere and climate and enabling their army to invade.