Enterprise stops at Cestus III, there to visit Commodore Travers, who enthusiastically invites Kirk to bring his key people to the surface. Beaming down, Kirk discovers the outpost has been destroyed! The landing party comes under attack, but Kirk and Spock recover a powerful ballistic weapon and strike back. The aliens flee, with Enterprise in hot pursuit, into an unknown region of space. There, both ships are paralyzed by an "unidentifiable power" from the distant star system of the Metrons, and both captains are transported to a world where they may engage in hand to hand combat to determine the fate of their respective ships. But is that the whole story?

Enterprise encounters an ion storm, which requires an observer in the ion pod. Top of the duty roster is Commander Ben Finney, who is tragically lost when Kirk must eject the pod as part of the Red Alert protocol. At the starbase, Commodore Stone discovers that the computer records tell a different story: that Kirk ejected the ion pod during Yellow Alert, and that if he had waited properly, Finney might still be alive. He offers Kirk a chance to resign his commission "for the good of the service", but Kirk refuses - and so draws a general court martial. His advocate? The quirky Samuel Cogley, who eschews his computer in favor of books.