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.

The Enterprise follows the wreckage of the S.S. Beagle to a planet where they discover an Earth-like civilization, except that Rome never fell, and rules a world much like twentieth century America. Intercepted radio transmissions suggest deeper mysteries, so Kirk, Spock and McCoy beam down to investigate, and then find themselves caught between the Roman government and a group of "sun worshippers". Proconsul Claudius wants Kirk to beam down his entire crew; the Proconsul is determined that no one will leave this world!