As in the 2009 film, multiple references are made to earlier events and the original timeline:
- The clothes Kirk and McCoy wear in the opening away mission are nearly identical to the ones they stole to infiltrate Paradise City in Star Trek V: The Final Frontier.
- In the first bar scene when Pike tracks down Kirk, a woman runs buy wearing the hairstyle of the Vulcan ambassador from Star Trek V.
- McCoy keeps a dead Tribble in the medbay.
- The USS Vengeance pays homage to a variety of Starfleet ship designs:
- It possesses a flat saucer section reminiscent of the USS Enterprise-D.
- Its nacelles are similar in shape to the re-fit USS Enterprise.
- Its stardrive section from the front bears similarities to the Excelsior class and the USS Enterprise-E, only painted black.
- Although the five year mission doesn't begin until the end of the film, the official IDW comic book series has established that by this point the Enterprise crew has experienced a number of the adventures and missions that, in the original timeline, took place during the five-year mission. Hence, the existence of a Tribble on the Enterprise now, rather than the doctor first encountering them later on.
- McCoy also throws in a reference to the Gorn.
- McCoy performs surgery on a photon torpedo with a science officer, again. This doubles as a Stealth Pun, a Stealth Visual Pun, or even a Shout-Out to the original Chris Rock act since the good doctor spends a great deal of his screen time performing 'Rocket Surgery'.
- Admiral Pike's line, "They gave her back to me. The Enterprise." is the same line (then) Admiral Kirk says to Scotty in Star Trek: The Motion Picture before boarding the Enterprise.
- A building known as "The Kelvin Memorial" can be seen in the background of one scene, referencing Kirk's father's doomed ship from the first movie.
- The ship used by the Enterprise crew to infiltrate Qo'noS was confiscated weeks before from someone named Mudd. Note: In a case of All There in the Manual, this is a not actually Harry Mudd, the conman from the original series. It is a reference to an event in the IDW comics prequel in which a female smuggler named Mudd (implied to possibly be the daughter of Harry) encountered the Enterprise crew.
- Khan and his crew being 300 years old, and responsible for a eugenics plot against the world, is a call back to Khan's backstory in "Space Seed".
- The black ops group behind Harrison and the Vengeance is Section 31, from Star Trek: Deep Space Nine and Star Trek: Enterprise.
- Admiral Marcus has the Phoenix, the NX-01, and a XCV-330 among his office collection of models depicting forms of Earth flight and space travel, from the Wright brothers' first plane through a V-2 rocket, Vostok, and Gemini.
- Also from Star Trek: Enterprise: the offshore stadium in San Francisco is still there, visible in at least one aerial shot of the city.
- There are numerous allusions to Star Trek II: The Wrath of Khan:
- Several lines and other elements from the climactic Separated by the Wall scene between Kirk and Spock in Wrath of Khan are re-enacted only with Spock and Kirk's places switched. Similarly, most of McCoy's lines from Wrath were transferred to Scotty whole cloth, specifically the lines, "You'll flood the whole compartment," and "Better get down here, better hurry."
- Spock repeats his famous line from Wrath of Khan during the opening away mission: "The needs of the many outweigh the needs of the few."
- Spock's echo of William Shatner's "KHAAAAAAAN!!!" line.
- Carol Marcus using her mother's last name to get on board the Enterprise recalls her son in the prime timeline using her last name instead of his father's. The last name Wallace is taken from Janet Wallace, a minor character in the TOS episode "The Deadly Years." Carol Marcus was originally intended to be Wallace in Wrath of Khan.
- Also, Carol telling her father that she's ashamed to be his daughter is the opposite of her son David telling Kirk that he's proud to be his son in The Wrath of Kahn.
- The Enterprise takes a massive beating by another Starfleet vessel, the USS Vengeance, leading to serious damage to the engineering section, just like how the Enterprise took a beating by the USS Reliant.
- Kirk incapacitates Scotty before going to repair the warp core, just like how Spock incapacitated McCoy under similar circumstances.
- Once again, Spock is the one to defeat Khan, except in the prime universe he used cold logic to exploit 2-D Space, whereas this time his Berserk Button has been hit and handles the matter much more... physically.
- The death of Admiral Marcus via head-crushing recalls the death-via-facial-strangulation of Admiral Dougherty from Star Trek: Insurrection.
- Kirk getting demoted for breaking regulations to save Spock recalls Star Trek III: The Search for Spock and Star Trek IV: The Voyage Home.
- Kirk still likes Beastie Boys, listening to "Body Movin'" during sex, referencing him listening to "Sabotage" as a kid in Star Trek (2009).
- Sulu takes the conn and has to act as temporary Captain, alluding to him becoming captain of the Excelsior in the original continuity. He also has to bluff to Harrison; Chekov did something similar in Star Trek V.
- Scotty manages to swiftly sabotage a really high-tech Starfleet prototype. Sound familiar?
- Harrison notes "No ship should go down without her captain", a line from Moby-Dick, a novel which Khan Noonien Singh loved, and which was also quoted in First Contact.
- At one point, Harrison threatens to incapacitate the Enterprise crew by depriving them of oxygen. Khan took over the Enterprise using this method in the TOS episode "Space Seed".
- Despite surviving a nerve pinch, phaser shots, and a lot of beating, Khan eventually goes down after Spock hits him with a piece of metal. Kirk likewise incapacitated him with an engineering tool in "Space Seed".
- This is not the first time that a starship has crashed into San Francisco Bay.
- On the approach to Qo'noS, a large broken moon fragment can be seen with a debris field stretching outward, suggesting that Praxis may have exploded early or was already in bad enough shape.
- Also, Uhura speaking Klingon may be a Take That! to the translator scene from Star Trek VI: The Undiscovered Country. Nichelle Nichols was unhappy that her character, a veteran communications officer, would not speak fluent Klingon. Perhaps as a nod to the original scene, Uhura does mention her Klingon is a little rusty.
- This is the second time in as many films that Chekov has saved Kirk and another crew member from falling to their deaths at the last second, but this time he managed it without the transporter.
- Kirk, Scotty and Chekov discuss how to save the day, which includes hitting a manual release located by the deflector dish. Chekov does it this time. Kirk still dies (sort of).
- Apparently, Starfleet likes to put key controls near the deflector dish.
- The "uninhabited" Ketha province? That's the same region General Martok spent his childhood in abject poverty.
- Kirk space jumps from the Enterprise to an enemy warship that is crippled. This time, it's not ridiculous because he actually has a spacesuit with thrusters attached so he can guide himself to an airlock.
- Carol mentions that Kirk once dated Christine Chapel, who is now serving as a nurse on a distant space station. Nurse Chapel was McCoy's assistant in the original series (and played by Gene Roddenberry's wife Majel Barrett), and who gets a mention in the Enterprise sickbay during the first film.
- One of the movie's tag lines was "Beyond the darkness, lies greatness," mirroring the tag line for Star Trek II: The Wrath of Khan "Beyond the darkness, beyond the human evolution, is Khan."
- Something of a meta example in the choice of Chekov as the Red Herring Shirt, as an early draft of Star Trek: The Motion Picture had him die during an attack on the Enterprise.
- The emergency meeting room Harrison attacks early in the movie is located in the Daystrom building.
- Though it's seen from a different angle, the Vengeance overtaking the Enterprise at warp, then attacking while still at warp, is eerily similar to the Scimitar doing the exact same to the Enterprise-E.
- Enterprise blatantly ignores orders and violates Klingon space.
- The construction bay that Scotty finds after being giving Harrison's coordinates looks eerily similar to a Borg Cube.
- Spock's violent beatdown of Khan at the end resembles him beating down Kirk in the first movie.
- Kirk at one point calls Scotty a "miracle worker". More or less Scotty's title in the original movies (from The Search for Spock onwards).
- Chekov is replaced as navigator by a bald woman.
- Along with heavy focus on his very measured deep voice, there were numerous closeups that focused of Benedict Cumberbatch's intense blue eyes and cold stare the opposite of Montalban Khan's very diplomatic and congenial facial expressions. This may be a tease based on the widespread fan speculation that he was being cast as a reimagined version of Gary Mitchell from "Where No Man Has Gone Before."
- Harrison's freakout when he thinks his crew is dead brings to mind Commander Kruge's when he tires to get his crew off the Enterprise before it blows up.
- The Big "NO!" included also recalls Ru'afo after the Enterprise crew thwarted his plans in Star Trek: Insurrection.
- A rendition of the original theme is played as the credits roll.
- Special effects for the film
include references to all five Star Trek series and one to Star Trek Online as well! - The Klingon part of the plot (a rogue Starfleet officer who doesn't believe in peaceful co-existence tries to incite a war between the Federation and an alien civilization) is quite similar to the Next Generation episode "The Wounded" as well as the John Ford novel The Final Reflection.
- The Shout-Out scene to The Godfather Part III also doubles as a Continuity Nod to the Star Trek: Voyager episode "Alliances", wherein the Trabe are pulling the same "shooting everyone through a window from an air vehicle" trick on the Kazon.
- This isn't the first time Kirk and Scotty have an adventure before returning to the Enterprise.
- Scotty has to yell at his assistant Keenser to get down from places that he shouldn't be sitting on...like an experimental torpedo.
- One of Qo'nos' moons is shattered; it appears that in this continuity, Praxis exploded several decades early.
