While out on patrol, the Terran starship ISS Enterprise, under the command of Captain Christopher Pike, encountered the First Federation vessel Fesarius. Pike wanted to claim the vast Fesarius for himself and sent his first officer, James T. Kirk, and a landing party over to acquire the vessel. They were greeted by Balok, but Kirk simply killed him and raided his laboratory for any useful technology. Years later, Balok's preserved body (along with Pavel Chekov's) was a prized possession of Kirk's. Balok's trademark smile was permanently preserved. (ST novel: Dark Victory)
By the year 2293, Balok lived on in the body of his puppet-being, which, in the counterpart universe, he had used as his disguise while facing the USS Enterprise. His Fesarius faced off against the ISS Excelsior, which was stealing its way through unfriendly space on a quest to find the end of the Janus Vortex, Janus Ultima, which held the key to allowing a displaced crew under Captain Hikaru Sulu to return to the counterpart universe USS Excelsior. (TOS video game: Shattered Universe)
The two sources were editorially unrelated, meaning there was no real effort made to explain how the deceased Balok's consciousness was transferred from his original body to the puppet-body.