Enterprise discovers a planet identical to Earth, with a very important exception: a few centuries earlier, a devasting plague struck. All of the adults were killed, but the children somehow survived - and still survive, hundreds of years later, feral and deeply distrustful of "grups". And there are monsters: insane, covered with scab-like plaques, they attack on sight. The disease is still active; the plaques appear on the landing party. If McCoy cannot discover a cure in the week they have left, all will die. Even Spock, now a carrier, cannot return to the ship.

Mapping star systems, Enterprise encounters an odd cube. Apparently solid, it senses the ship, moves to block it - and when Enterprise attempts to disengage, pursues while emitting dangerous radiation. Kirk is forced to order its destruction. He probes farther, to find the builders of the device. And he does, when the Fesarius appears. The immense flag ship of the First Federation and her captain, the enigmatic Balok, regard the destruction of the cube as an aggressive act, and determine that the crew will be imprisoned and the ship destroyed.