Historian and sociologist John Gill has stopped responding to transmissions. He is embedded in the Ekosian population to study it. Investigating, Kirk and Spock discover that Ekos has developed nuclear weapons - an achievement well ahead of where they should be scientifically, based on past probes. And they have modeled their society on Nazi Germany, right down to oppression of their sister planet, Zeon. It seems apparent Gill has contaminated this society, but why? And why Nazi Germany?

Enterprise discovers her sister ship, Exeter in orbit around a planet, unresponsive. Kirk, Spock and McCoy beam aboard and discover only empty uniforms mixed with a handful of crystals. Then they find a log - the ship is infected with a deadly plague! Their only chance is to beam down to the planet's surface immediately. There, they discover heartbreaking evidence that Exeter's captain Ronald Tracy has violated the prime directive, up to and including mass murder. But he has what he believes is a good reason - and it depends on McCoy's research into a long ago bacteriological war.