Lieutenant Commander Montgomery Scott remained chief engineer and third in command of the U.S.S. Enterprise throughout 2269, the final year of the starship's famed five-year voyage of exploration. As ever, Scott's beloved engines remained his primary sphere of interest. Scott assumed command of the Enterprise on stardate 5483.7 (2269), when Captain Kirk and Commander Spock were on the surface of the second planet of the Taurean system, where they had been captured by that world's desperate female population, who periodically lured the men of passing starships to them in order to drain their life forces for sustenance. Because Scott, being male, was no less under the influence of the Taurean women than were the captain and first officer, Lieutenant Uhura temporarily relieved him of command and organized the rescue team that recovered Kirk and the rest of his landing party. During this crisis, Scott's preoccupation with engineering gave way to a desire to sing traditional Scottish songs, thereby revealing that the chief engineer possessed a more than passable singing voice.

After the conclusion of the Enterprise's historic five-year mission, Scott stayed in Starfleet and received a promotion to full commander. He subsequently presided over the 18-month refit of the Enterprise, under the command of Captain Willard Decker. This renovation was completed on stardate 7412.3 (2271), just in time to allow Admiral James Kirk to resume command of the starship during the V'Ger crisis — with Montgomery Scott attending her engine room, the only place in the universe he truly regarded as home. Montgomery Scott retired from Starfleet on approximately stardate 9524.0 (2293) with the final rank of captain, and ended up stranded in the 24th century on stardate 46125.3 (2369) after spending more than 76 years dematerialized inside a transporter buffer in order to survive the crash his transport ship, the U.S.S. Jenolen.