By the mid-23rd century, Zeon had been living in peace for many generations, and had developed spacecraft designed for interplanetary spaceflight. Noticing the condition of anarchy among the warlike, pre-spaceflight Ekosians, many Zeons came to Ekos in an effort to help their neighbors learn peaceful ways. Sometime after 2218, a Zeon colony was established on Ekos.
After the cultural contamination of John Gill and the takeover of the Nazi regime by Melakon, Zeons became a hunted people on Ekos. Using the Nazi model, Melakon used the presence of Zeons in much the same way as Adolf Hitler used the Jews of Germany and Europe, scapegoats to be blamed for Ekos' problems and eventually a threat to be eliminated. With the technology elicited from Gill, Melakon rapidly upgraded Ekosian weapons. By 2268, the "Final Decision", an genocidal invasion on the planet Zeon, was preparing for deployment.
The USS Enterprise, assigned to discover what had happened to John Gill, arrived just before the launch of the invasion against Zeon. The intervention of Kirk, Spock and McCoy roused Gill in time to call-off the attack, and Gill recanted his beliefs to Kirk as he died, insisting that the Prime Directive was "the only way".
The regime created by Gill and Melakon proved to be weaker than their German model. The Nazi government and the "Final Decision" was not embraced by all of Ekos. An underground alliance of Zeons and Ekosians had formed, including high-level Nazi party members who wanted no part in the genocide. Kirk's actions allowed the Zeon Isak to kill Deputy Führer Melakon. Afterward, there appeared to be no impediment to the two worlds working together. Spock observed that the union of the two cultures would make a fine addition to the Federation. (TOS: "Patterns of Force")
The Star Trek Compendium (3rd ed., p. 98) states the name "Zeon" is drawn from "Zion," the ancient Hebrew designation for Jerusalem, from which the political movement "Zionism" is derived. Also, the character names were variants of Biblical figures: Abrom for Abraham, Isak for Isaac, and Davod for David.