South Park has made several references to the Star Trek franchise over the years. To date, Star Trek references have been featured in 29 episodes.
- Stan tells Jesus "Someone once said Don't try to be a great man, just be a man." When Jesus asks who said it, Stan replies "you did, Jesus." This was from the movie Star Trek: First Contact. When Kyle asks if that was in the Bible, Stan says he saw it on Star Trek.
- Cartman's line "Sure! Captain Ahab has to get his whale, huh?" is an almost direct quote from Star Trek: First Contact, which in turn is a reference to Herman Melville's novel Moby-Dick.
- "City on the Edge of Forever (Flashbacks)" is the name of a Star Trek episode. One of the kids on the school bus was wearing the Enterprise mission patch and a red shirt. On Star Trek the characters in red shirts are usually first to be killed when a situation gets dangerous.
- When Robert Redford throws Mr. Hankey against a wall, he says "I have had enough of you!" in a similar way to the way James Kirk said it in Star Trek III, as he kicked the Klingon Kruge off a cliff and into a lava flow.
- The episode is a parody of the original Star Trek episode, "Dagger of the Mind".
- The bearded Stan, Kyle, and Cartman from the parallel universe are an obvious reference to the Star Trek episode, "Mirror, Mirror", where the mirror universe Spock wore a beard.
- In a joke reminiscent of the first Star Trek reference on the show, Stan tells his father that the Bible says "The needs of the many outweigh the needs of the few." When Kyle again corrects him and attributes the quote to Star Trek II: The Wrath of Khan, Stan says "The Bible, Wrath of Khan, what's the difference?"
- When Satan throws Saddam Hussein back into Hell, he says "I have had enough of you!" This echoes Kirk's line from Star Trek III: The Search for Spock, when he kicks the Klingon captain off the cliff (again, to a fiery death).
- The discussion about love and public school between Kyle and Rebecca Cotswolds is almost word-for-word the discussion between Captain Kirk and Shahna from "The Gamesters of Triskelion", complete with the Star Trek "love theme" ("Ruth") playing the background.
- As he watches the start of Sarque du Son Blue, a bored Eric Cartman tells himself "we've reached fag factor 5, captain."
- Randy's fit of rage, ending in him smashing the glass doors of the living room cabinet and shouting "No! Nooo!!" is very similar to a scene in Star Trek: First Contact, where Captain Picard does the same. In fact, Randy's voice changes from Parker's to a sampling of Patrick Stewart's voice from the film.
- The boys try to figure out how to go back in time, so they meet with a pair of scientists that debate the two schools of thought for time travel, the Spock Theory (slingshot around the sun, as seen in the episode "Tomorrow is Yesterday") and the Lieutenant Commander Data Theory (magnetic vibration, as seen in the episode "Time's Arrow"). One of the scientists warns that time travel is tricky, saying "four times the Enterprise traveled back in time and four times they almost didn't make it back."
- This episode references a "Geek Debate" attempting to determine how many episodes of Star Trek exist. The debate centers on the status of the episode, "The Menagerie". Additionally, both numbers of episodes quoted by the geeks (72 and 73) are incorrect; the disputed numbers are, in actuality, 78 and 79.
- "The before time", "no foolies" and the Shatner-esque speech are references to the "Miri" episode of Star Trek.
- When Token brings a DVD of The Lion King rather than a VHS copy, Cartman quips "Let me take this disc up to the Enterprise and see if Captain Kirk can decrypt it."
- The scene where a man tells Maury that “the ratings have just started to plummet” is a play on the original Star Trek series, where crew members often viewed computer displays in such a way. The man also bears an uncanny resemblance to Leonard Nimoy.
- Michael Dorn is famous for playing Worf on Star Trek: The Next Generation and Star Trek: Deep Space Nine. He is portrayed in this episode wearing a sweatshirt which bears the logo of Pasadena City College, his real-life alma mater. After this episode aired, Dorn revealed that he is a fan of South Park, and would've provided his voice for the episode had he been asked.
- One of the knives on display looks like a "Klingon" knife.
- Mel Gibson chases after a bus, recreating the famous truck chase scene from Mad Max 2, also honking his horn and shouting "Qapla!" (in reference to Star Trek) to get his $18 back
- In the beginning of the episode, the four boys are role-playing as Star Trek characters. Cartman plays the captain, and refers to his friends as "First Officer Stan," "Engineer Kenny," and "Vulcan Jew Kyle".
- Miss Claridge's wheelchair and condition are based on that of the fictional Captain Christopher Pike from the Star Trek: The Original Series episode, "The Menagerie".
- The scene in which Kyle reveals he had hidden the real egg and replaces the one "killed" by the assassin references Star Trek. Kyle asks Stan if he really thinks his hat is stupid (a comment made by Stan over the phone earlier in the episode). Stan approaches Kyle, and says: "As a matter of fact, I think it is the nicest hat I have ever known". Stan uses exactly the same intonation and style of Captain Picard in Star Trek: First Contact, when he apologizes to Mr. Worf after calling him a coward by saying: "In fact, I think you're the bravest man I have ever known".
- In one of the Family Guy cutaways, Peter Griffin plays Captain and Tenille songs with Captain Kirk.
- When the FOX Network executive gives the order to pull a Family Guy episode from airing, he gives the destruct code of the Enterprise from original Star Trek series episode, "Let That Be Your Last Battlefield", later reused in Star Trek III: The Search for Spock.
- Captain Kirk and Star Trek villain Khan Noonien Singh are residents of Imaginationland.
- Craig Tucker paraphrases Montgomery "Scotty" Scott, Chief Engineer of the USS Enterprise when he says, "Aye, and if my grandmother had wheels, she'd be a wagon!" Upon seeing the new Starship design in Star Trek III: The Search for Spock.
- Star Trek: First Contact is mentioned by name by the news reporter.
- The Space-Cops ship design is the same as the Vulcan's ship at the end of Star Trek: First Contact .
- The Vulcan Surface from Amok Time is used by the Geniuses to convert Gerald to Apple.
- When Funnybot begins overloading, it screams "Analyze!... Analyze!" This is a reference to the demise of the probe Nomad from the original series episode, "The Changling". Kyle suggests that Funnybot could be defeated by a logic loop, which is similar to how Nomad was defeated. He is also carted away using the same anti-gravity devices used in the same episode. The use of a logic loop was also used to defeat an android in the episode "I, Mudd".
- Eric Cartman attempts to recruit the "Kids who play Star Trek" into buying the Playstation 4 video game console with his "Game of Thrones" group . He mocks them by calling them dorks and gay. He signs off with "Uh yeah, big dong and prosper" instead of the popular phrase "Live long and prosper".
- When Randy is in his living room relaxing and eating Memberberries, the fruit makes references to Spock and tricorders.