While on a planet in the Omega system trying to find ryetalyn to stop an epidemic of Rigellian Fever, Kirk, Spock and McCoy come into contact with a strange man, Flint, that didn't register on their previous sensor scans of the planet surface. Flint seems to know much about the ancient history of Earth which leads to some startling discoveries.

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.