In the original script, Lazarus romantically came on to Lt. Charlene Masters to gain her assistance. The two subsequently fell in love, but when African-American actress Janet MacLachlan was cast as Masters, the romantic angle was dropped. In addition, Gene Roddenberry considered it too similar to the romance between Khan and McGivers in Star Trek: Space Seed (1967). As stated by Roddenberry in a Season One memo: "In both 'Space Seed' and this story, we have a crew woman madly in love with a brawny guest star and flipping our whole gang into a real mess because she is in love... do they have to do [this] in two of our scripts?"
John Drew Barrymore was originally cast as Lazarus, but failed to show up for shooting and had to be replaced by Robert Brown, causing the episode to go two days over schedule. Star Trek (1966)'s producers subsequently filed and won a grievance with the Screen Actors Guild, which suspended Barrymore's SAG membership for 6 months.
Actor Eddie Paskey appeared in 59 episodes of the original Star Trek (1966) series, 50 of them playing Lt. Leslie - a character name that came from William Shatner himself inserting his eldest daughter's first name (Leslie) into the show - but only in 'The Alternative Factor' does Eddie's role as Lt. Leslie ever appear in closing credits, and when it does - in contrast to the spelling by which it has become widely known and accepted - it is spelled L-E-S-L-E-Y.
James Doohan and George Takei do not appear in this episode. For unknown reasons Scotty and Sulu were substituted in the roles of engineer and helmsman by Charlene Masters and Mr. Leslie, respectively.
Lazarus manipulates several components in a "high voltage" access tray in order to create an overload, and eventually steal several dilithium crystals. These objects are simply dual banana plugs often used by electronics technicians.
After John Drew Barrymore failed to show up on the set, director Gerd Oswald decided to shoot scenes which didn't involve his character. On the second day, it was decided to either shut down production and scrap the episode overall or find a replacement. Rob Brown was literally dragged in to the set, right after he agreed to play the role. He recounted the filming to be very tight and tense.
The footage of the two Lazaruses fighting was created by filming two stuntmen fighting in a smoke-filled room with orange and purple walls, then double-exposing its colour negative footage over an astronomical photograph of the Trifid Nebula.
Unlike in the earlier Star Trek: Mudd's Women (1966), dilithium crystals are portrayed here as translucent amber slabs, which conveniently fit in the energy panels of Lazarus' ship. The universality of the amber-slab dilithium crystal mount connector as being common to both the Enterprise and to Lazarus' timeship, suggests a commonality in the manufacture and sourcing of at least its dilithium crystal converter assembly. There is also no mention in this episode of bypass circuits being fused beyond useabilty as a power-conversion alternative, the existence of which were mentioned to bolster the direness of the need for replacement crystals in the storyline of Star Trek: Mudd's Women (1966). Dilithium crystals, in their natural state, however, are depicted as resembling quartz crystals in both Star Trek: Mudd's Women (1966) and Star Trek: Elaan of Troyius (1968), suggesting that the amber-slab devices depicted in this episode are themselves some kind of mounting structure, the translucent glow meant to depict the power flow somehow being transformed by being focused through the crystal or crystals contained within. The amber slabs are, however, explicitly referred to in dialogue as being the crystals themselves.
Depending on which version of this episode you watch, the closing stills change. The original syndicated version and the VHS version show the still as the Enterprise leaving the Earth-like planet from Star Trek: Miri (1966), however, the Sci-fi Channel and DVD version show the still as just a blue planet, possibly Rigel 12 from Star Trek: Mudd's Women (1966) or Starbase 11 from Star Trek: Court Martial (1967).
Periodically throughout the episode, the two versions of Lazarus exchange places. One of them has a wound or bandage on his head which McCoy treated: this is the "insane" Lazarus from our universe; the other is his rational counterpart from the antimatter universe.
A still image in the closing credits of Star Trek: The Squire of Gothos (1967) shows the corridor between universes set unaltered by the effects and double exposure. Titled at a 45 degree angle, William Shatner stands ankle deep in smoke in a near pose of the crucifixion, falling back into a purple corridor, where an orange line draws the horizon to a vanishing point.
Along with Star Trek: Friday's Child (1967), this is one of the only two episodes where outdoor planet scenes were filmed both on Desilu Stage 10 and on location (both times at Vasquez Rocks). Originally, all planet-side scenes were scheduled to be filmed on location, but due to the turmoil during production, director Gerd Oswald couldn't finish shooting at Vasquez. Matt Jefferies and the art department prepared a spot on Stage 10 which could accomodate the missing "alternate universe" sequence.
The shot of the Enterprise destroying Lazarus' ship is unique on three counts. First, it is the only time the Enterprise is seen from behind as it fires phasers. Second, it is the only time that the ship fires a single beam (as opposed to the usual two). Finally, it is the only time that the phasers make no noise - at least when the beam is seen in space.
This episode introduces a new set, a small subsection of engineering, described in the final draft of the script, dated 11 November 1966, as the "Lithium [sic] Crystal Recharging Section", which was described as "A portion of Engineering where there are bins into which dilithium crystals are placed for recharging."