All of this cost money. The standard television episode budget of the mid-1960s was designed around shows that could be produced largely on existing sets with minimal visual effects. *Star Trek* was pushing against that budget constraint in every episode.
Matt Jefferies, the production designer, became extraordinarily inventive in managing these constraints. The bridge set was designed to be multifunctional — the same physical space, shot from different angles and with different elements added or removed, could represent multiple locations on the ship. The alien planets that appeared each week were largely the Desilu back lot redressed with specific props and atmospheric lighting. The alien creatures were achieved through actor makeup, limiting the number and type of non-human characters the show could include but allowing a range that would otherwise have been unaffordable.
Robert Justman’s production management was focused on making episodes that looked more expensive than they were. The specific tricks of television production efficiency — the use of the same set pieces in multiple episodes, the careful management of makeup hours, the scheduling of effects-heavy sequences to minimize cost — were applied throughout. The result was a show that, by most viewer assessments, looked like it cost more than it did.
The overruns were real anyway. Even with Jefferies’s design efficiency and Justman’s production management, *Star Trek* consistently exceeded its per-episode budget. The gap was absorbed by Desilu during the series’ run; it was part of the deficit that the studio was carrying against eventual syndication returns that never arrived under its ownership.