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After production on the film was completed and a month before the film's release, Anton Yelchin died in a freak car accident. During the ending credits, there is a dedication caption which reads, "For Anton".
The reference about the USS Franklin coming to be on the planet by "some green space hand" is a reference to the episode Star Trek: Who Mourns for Adonais? (1967).
Simon Pegg identified the space station as "Starbase Yorktown" in early interviews. "Yorktown" was the original name of the starship in Gene Roddenberry's early script treatments for the original Star Trek (1966) series, before this was changed to "Enterprise".
When Kirk and crew first enter Yorktown's reception area, an announcement can be heard over the intercom referring to a starship with registry number NCC-2893 just arriving. This is a reference to the USS Stargazer (NCC-2893), the first ship that Captain Jean-Luc Picard commanded on Star Trek: The Next Generation (1987).
Simon Pegg revealed in a press conference that the character Jaylah, was inspired by Jennifer Lawrence in the film Winter's Bone (2010). "We were trying to create this very independent character. But we didn't have a name for it," Pegg said. "So we just called it 'Jennifer-Lawrence-In-Winter's-Bone.'" "That's a long name," the writer and actor joked. "So it started getting tiring always saying, well Jennifer-Lawrence-In-Winter's-Bone is fighting here. So then we started calling her J-Law. And then she became Jaylah."
A montage of images of the Enterprise traveling the galaxy plays over the closing credits; among these is a brief glimpse of the "giant green space hand" previously mentioned by Mr. Scott.
Alice Eve does not return as Dr. Carol Marcus. During this film, she is not mentioned and her absence is unexplained. In the ending of the previous film Star Trek Into Darkness (2013), Carol became a member of the Enterprise crew and joined them on their five-year mission.
McCoy and Kirk toast to "perfect eyesight and a full head of hair", a reference to Star Trek II: The Wrath of Khan (1982) where Kirk needed glasses due to old age as well as William Shatner's toupee.
In an interview, Karl Urban stated that he almost did not return to the role of Dr. Leonard "Bones" McCoy. What convinced him to stay was a discussion with director Justin Lin.
A reference is made to the episode Star Trek: The Trouble with Tribbles (1967): When McCoy remarks to Kirk that he "took this from Chekov's locker" (referring to the bottle of alcohol), Kirk responds to the effect "I would have pegged Chekov as a vodka man..." as both are surprised by the type of alcohol that Chekov drinks. This is confirmed as scotch in the final party scene when Chekov remarks that "It was invented by a little old lady in Russia". In the original episode, Chekov and Scotty sit in the Space Station K-7 bar as Scotty states that Chekov "get off that milk diet" and have scotch instead since it was "a drink for a man". Chekov replies that "it was invented by a little old lady from Leningrad".
The limited edition poster which features Kirk, Spock and Jaylah is a homage to the original poster for Star Trek: The Motion Picture (1979) with Kirk, Spock and Ilia.
The USS Franklin's registry number NX-326 pays homage to Leonard Nimoy as his birthday is March 26 or 3-26.
According to Zachary Quinto, while he greatly enjoys the character Spock, he has made mention that he is ready to move on from the role and venture into other projects. He has stated though that he fully plans to finish out his contractual obligations in playing the role of Spock and seeing where his character's journey goes in the trilogy. Quinto (just like the rest of his main co-stars) signed on for a three picture deal, which makes this film his last contractual commitment towards the role of Spock. However, he has since signed on for a fourth movie.
A renegotiation of contracts has meant a larger pay deal for the returning actors, while also writing in the option of Chris Pine and Zachary Quinto returning for a fourth film.
In this film, Sulu (John Cho) is revealed to have a daughter. In Star Trek: Generations (1994), Sulu (George Takei) is also revealed to have a daughter (she operates the helm on the Enterprise-B).
Writer Simon Pegg and director Justin Lin made the decision of making Sulu gay as a nod to original actor George Takei, who has since become a prominent LGBT rights activist. However, Takei has since stated his disagreement with this decision as that was not Gene Roddenberry's intention for the character Hikaru Sulu.
The Enterprise is on the 966th day of its five-year mission. 966 plays homage to when Star Trek (1966) first aired, September 1966.
J.J. Abrams declined to return to direct the third film because of his directorial obligations on Star Wars: Episode VII - The Force Awakens (2015). Abrams stayed on as a producer for the third film while screenwriter Roberto Orci - one of the writers for the first two installments of the newly rebooted franchise - was initially chosen to direct the third installment which later on changed to Justin Lin .
In August 2014, this was announced that Paramount Pictures has pushed back the film's release in time for the 50th anniversary celebration of the late Gene Roddenberry's original series.
The first Star Trek film ever to be shot primarily in Vancouver, British Columbia and not in Hollywood. All existing sets, including those of the USS Enterprise, will be rebuilt from scratch in a large studio in Vancouver.
When Kirk asks Sulu if he can fly the USS Franklin, Sulu turns and says, rather incredulously "Are you kidding me?". Repeating a line, with the same expression and tone, that Captain Sulu (George Takei) used, in Star Trek VI: The Undiscovered Country (1991).
This is Anton Yelchin's final Star Trek film before his death on June 19, 2016 at age 27.
The first Star Trek feature to be shot entirely digitally, as well as the first since Star Trek VI: The Undiscovered Country (1991) not shot with Panavision anamorphic lenses.
Simon Pegg revealed on The Graham Norton Show (2007) that he was involved in the writing process for this movie, and on May 19, 2015, on his website, he referred to the title as "Star Trek Beyond".
The character Commodore Paris is a likely nod to Lieutenant Tom Paris and his father Admiral Owen Paris on Star Trek: Voyager (1995).
The USS Franklin (NX-326) is named after Justin Lin's father Frank Lin.
In a July 2016 interview in New York magazine, John Cho said that it was important to him for Sulu's husband, Ben, to be Asian also: "Early on I said to Justin Lin, 'Dude, it would be important to me to have an Asian husband.' Basically, it was a little Valentine to the gay Asian friends that I grew up with. This may be presumptuous, but I always felt the Asian gay men that I knew had much heavier cultural-shame issues. This is probably more so for my generation than for yours [meaning New York interviewer E. Alex Jung], but I felt like those guys didn't date Asian men because of that cultural shame. So I wanted it to seem really normal in the future. I thought that would be the most normal thing, that there was zero shame in the future. I don't know if that hit or not, but it was something that I felt in my gut and asked for that... Justin was [receptive]. There was talk of, 'Should he have a human husband?' So it went that far. I wanted that relationship to feel super familiar, you know what I'm saying? I didn't want to push the difference envelope; I just wanted it to be very, very traditional looking. There was something about this pairing that would seem very old-fashioned, and then something about it to gay men that would be radical." Cho also said that it was very hard to find an East Asian actor in Dubai (where they were shooting) who would agree to play a gay man: "We had a guy and then his parents really objected. Basically, we couldn't find an Asian actor willing to play gay in Dubai is my understanding." So they ended up enlisting the co-screenwriter Doug Jung, who is not a professional actor, to play the role.
This film takes place two and a half years after Star Trek Into Darkness (2013).
Throughout Star Trek history, we have heard about warp fields or a static warp bubble, but in this movie you actually get to see this, when the Enterprise is warping. The ship's nacelles create a warp field that surrounds the ship and moves the space around the ship, while actually the ship is standing still. Warp drive has been considered like ride a surf board in many articles. The ship does not move, but space around her does. Scotty even says this in the reboot, when he mentions in his transwarp theory, he never thought of space to be the thing that was moving.
Early in the film, Kirk mentions that the five-year mission had begun to feel "episodic" - an obvious nod to the episodic nature of the original (and subsequent) series.
The Franklin's dedication plaque lists it as a Starship class vessel. This was the original class of the Enterprise from the pilot of Star Trek (1966), before this was changed to the canon Constitution class. Some references in Star Trek lore, such as technical manuals and novels, still refer to the original Enterprise as a Starship class. The name Constitution class was only ever mentioned by the characters twice, in the episodes Star Trek: The Next Generation: Relics (1992) (which guest starred James Doohan, the original Scotty) and Star Trek: Deep Space Nine: Trials and Tribble-ations (1996).
Producer Trademark (J.J. Abrams): [Kelvin]: When the Enterprise crew are abandoning the ship, Kirk says, "Get in your Kelvin Pods." This is a reference to Abrams' grandfather and role model, Harry Kelvin.
A man named James Kirk is the lead FX technical director in this film.
This film takes place in March 2263. In that year, the following events happened in the original timeline:
  • Ben Childress, Herm Gossett, and Benton partner up to establish a mining company on Rigel XII (This was shown in Star Trek: Mudd's Women (1966).

  • One hundred fifty men, women and children led by a man called Elias Sandoval depart Earth and travel to Omicron Ceti III, to establish the future Omicron colony (this was shown in Star Trek: This Side of Paradise (1967).

  • A child Lactran, who later was encountered by the USS Enterprise landing party in 2269, is born on Lactra VII (this was shown in Star Trek: The Animated Series: The Eye of the Beholder (1974).

This is Greg Grunberg's second Star Trek film in the reboot series but only his first on-screen appearance as Commander Finnegan. He played young James T. Kirk's stepfather in the Star Trek (2009) reboot. However, only his voice was heard in the antique convertible that Kirk drives off the cliff.
Justin Lin took the directing job of the third film by beating out Edgar Wright, Rupert Wyatt, Morten Tyldum, Daniel Espinosa and Duncan Jones.
At 9 mins. 33 secs. into the film, there is a scene in which two trains pass by and the frame cuts to an Orion child. This is Justin Lin's son, whom he used in his previous Fast and Furious films; the scene where Dom and Brian are pulling the safe and the scene where Letty is racing Dom in London, respectively.
The bottle of Saurian brandy that Kirk is drinking is similarly shaped to the bottle of Saurian brandy found on McCoy's sickbay shelf on Star Trek (1966).
After Star Trek: Insurrection (1998), this is the second "Star Trek" film not to feature any scenes on or near Earth.
At one point towards the climax of the film, Spock is giving a detailed explanation. Kirk interrupts him saying "Spock, skip to the end." This is a reference by Simon Pegg to his sitcom Spaced (1999). In which Tim Bisley (Pegg) cuts off Daisey Steiner (Jessica Hynes) saying the line "Skip to the end", once in each season of the series.
There is a reference to Star Trek: The Lights of Zetar (1969) during the deleted scene where Scotty and Kirk have just arrived at Starbase Yorktown. After being asked for a drink by Kirk, Scotty says he is already going for a drink with "Lieutenant Romaine", so Kirk declines. Lieutenant Mira Romaine was a woman Scotty fell in love with during "The Lights of Zetar".
Music from the episode Star Trek: Shore Leave (1966) can be heard when Kirk and Chekov are caught in Jaylah's trap.
The film was released 50 years after Star Trek (1966) premiered for the first time on American television. 30 years after the release of Star Trek IV: The Voyage Home (1986), 25 years after the release of Star Trek VI: The Undiscovered Country (1991) and 20 years after the release of Star Trek: First Contact (1996).
McCoy and Kirk share an early birthday drink where McCoy toasts to perfect eyesight. This is a nod to Star Trek II: The Wrath of Khan (1982), which also happens near Kirk, where McCoy give Kirk glasses for his birthday.
When Kirk and McCoy toast Jim's birthday, Kirk comments that the Saurian Brandy comes from the planet Thasus, which played a pivotal role in Star Trek: Charlie X (1966).
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Justin Lin's first Sci-Fi directorial movie.
On the original Star Trek (1966) series, at the end of the introductory speech, narrated by William Shatner at the beginning of each episode, is "to boldly go where no man has gone before." On Star Trek: The Next Generation (1987), narrated by Patrick Stewart, it was substituted for the words "to boldly go where no one has gone before", in an effort to be more gender-neutral and race-neutral. In this feature, the otherwise introductory speech is moved to the end and narrated by multiple members of the cast, the last bit ("to boldly go where no one has gone before") being spoken by a female character, Lieutenant Uhura, portrayed by Zoe Saldana
James T. Kirk turns 30 years old in Star Trek Beyond. In Star Trek (2009), Captain Robau told the Romulans that the current stardate was 22.33.04. That was the date of George Kirk's death and James T. Kirk's birth. James T. Kirk's captain's log in Star Trek Beyond reveals the current stardate 22.63.04.
With the release of this film, all three "main villains" in the rebooted Star Trek series have been played by an actor who has also portrayed a Marvel Comics superhero on film. Eric Bana from the Star Trek (2009) reboot had previously portrayed Dr. Bruce Banner in Hulk (2003). Benedict Cumberbatch has portrayed Dr. Stephen Strange in Doctor Strange (2016). Idris Elba had previously portrayed Heimdall in Thor (2011) and its follow ups.
In a July 7, 2016 interview in Australia's Herald Sun newspaper, John Cho said that in this third movie in the rebooted Star Trek series, his character, Hikaru Sulu, is revealed to be gay and raising a daughter with his husband. Cho told the Herald Sun's James Wigney that the film's director, Justin Lin, and co-writer, Simon Pegg, decided to identify Sulu as gay as a tribute to George Takei, the openly gay actor who played Sulu on the original series and movies.
This is the second time that Star Trek and Star Wars have released movies in the same year, alongside the release of Rogue One (2016). The first time this happened was in 2002, with the releases of Star Trek: Nemesis (2002) and Star Wars: Episode II - Attack of the Clones (2002). Both Star Trek Beyond (2016) and Star Wars: Episode VII - The Force Awakens (2015) feature Greg Grunberg as a cast member.
The first Star Trek film to be directed by a director who was born after the year the original Star Trek (1966) series aired. J.J. Abrams was born a few months after the first episode aired on television, while Justin Lin was born four years after the series ended.
The first production, since the original Star Trek (1966) series, where a bulk of the filming was shot outside of California, in fact off the Paramount Studios lot.
Between takes, the cast did dubsmashes to pass the time. The cast mostly agreed that John Cho (Hikaru Sulu) is the so-called "Dubsmash King".
Kirk states in his log that they are on their "966th day in deep space - A little under three years into our five-year mission". The original Star Trek (1966) series ran for only three seasons, from September 8, 1966 until June 3, 1969 (2 years, 8 months, 25 days, also "a little under three years") before being cancelled.
This film shows a romantic relationship between Spock and Uhura. On the original Star Trek (1966), Uhura has a thing for Captain Kirk, while Spock and Nurse Chapel are shown to have a romantic inclination towards one another. Through the original series, Spock can be seen having romantic relationships with several guest stars.
Reunites director Justin Lin with Indonesian actor Joe Taslim, who first worked together on Furious 6 (2013) as Jah.
WILHELM SCREAM: When the aliens board the Enterprise, and an alien throws a crew member over a walkway railing.
Simon Pegg wrote most of Jaylah's dialogue in broken English based on Sofia Boutella's French accent.
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When Spock is looking at Spock Prime's history, this mentions his Starfleet record. Spock Prime was second officer of the Enterprise in the original pilot episode Star Trek: The Cage (1986). Majel Barrett was "Number One" or the first officer. Spock was the first officer under James T. Kirk for the rest of the original Star Trek (1966) series.
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Claudio Miranda was hired as cinematographer by Roberto Orci when he was scheduled to direct but left the production after Orci stepped down and was replaced by Stephen F. Windon.
In July 2016, this was announced online that Chris Hemsworth would return as Lt. George Kirk in Star Trek 4. This is most likely the fourth film that will be released in 2019 to mark the tenth anniversary of Star Trek (2009).
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On December 23, 2014, Paramount Pictures announced that the film was to be released on July 8, 2016. On September 17, 2015, Paramount Pictures has pushed back the film's release date to July 22, 2016.
Justin Lin is the youngest director to direct a "Star Trek" film. He was born in 1973, four years after Star Trek (1966) ended.
When J.J. Abrams dropped out of the director's position, Joe Cornish, Jon M. Chu and Brad Bird were considered to direct when the project was in early development.
The song "Sabotage" was also played in This Means War (2012), starring Chris Pine and Tom Hardy. Tom Hardy played Praetor Shinzon, the main villain in Star Trek: Nemesis (2002).
The scene where McCoy and Kirk comment that they thought Chekov would be a 'vodka guy' is a reference to Chekov's character plot-wise being ethnically Russian in origin and Russians' fondness for consuming vodka. A line towards the film's very ending is connected to the scene whereas Chekov states, "Do you knew that Scotch was actually invented by a little lady in Russia?"
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Zachary Quinto and Greg Grunberg both starred together on Heroes (2006), although they have no scenes together in Star Trek Beyond (2016).
Reunites director Justin Lin with actor John Cho, who first worked together on Shopping for Fangs (1997).
This film's plot is almost similar to a rejected outline for Star Trek VI: The Undiscovered Country (1991) which was written by Walter Koenig, which Spock and the new Enterprise crew are captured by a race of worm-like aliens and Captain Kirk and the old crew are forced out of retirement to rescue them.
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In the digital schematic of Starbase Yorktown, the central sphere bears an uncanny resemblance to the Death Star from Star Wars: Episode IV - A New Hope (1977).
Enemy Mine (1985) has been considered a possible influence behind this film, where the Enterprise crew are stranded on an alien planet when they are attacked by hostile natives.
The motorcycle sequence was a nod to the Fast and the Furious films. Justin Lin directed the later Fast and the Furious films.
The disruption frequency of 57.7 is likely a nod to the premier date of the original Star Wars: Episode IV - A New Hope (1977) in May 1977.
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Beats out the Friday the 13th franchise with its thirteenth film, although the first eight films were produced by Paramount Pictures, the later two films, Freddy vs. Jason (2003) and the Friday the 13th (2009) reboot were produced by New Line Cinema/Warner Bros.
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Diverse members of the cast belongs to another franchises:
The film's teaser trailer was released on December 14, 2015.
This marks the fifth collaboration between director Justin Lin and costume designer Sanja Milkovic Hays after working together before in the Fast and the Furious films. This is also the second time Hays has been involved on a Star Trek film after working on Star Trek: Insurrection (1998).
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The film's original theatrical trailer was released on May 20, 2016.
Zoe Saldana and Idris Elba had previously worked together in The Losers (2010). Their co-star in that film Jeffrey Dean Morgan had played one of the Xindi that Edison is said to have fought in Star Trek: Enterprise: Carpenter Street (2003).
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The film's second theatrical trailer was released on June 27, 2016.
This is the second J.J. Abrams produced Star Trek film where decades-old abandoned mining equipment is used as a superior weapon against Starfleet.
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Fiona Vroom: the titular guest star of Star Trek Continues: Lolani (2014) appears as an Orion crew member during the Captain's Log scene near the beginning of this film.


The trivia items below may give away important plot points.

According to Idris Elba in a Facebook live chat with Zoe Saldana, the black eye that Chris Pine has in the final fight scene with Idris Elba is not makeup, it's a real black eye that Pine got when they got a little too rough during filming.
The toast Kirk makes to absent friends at the very end is immediately followed by a shot on Anton Yelchin, who tragically passed away on June 19, 2016.
Zachary Quinto brought real emotion to the scenes which Spock learns Spock Prime has died and talks about him. Zachary Quinto and Leonard Nimoy were good friends in real life and Nimoy was Quinto's mentor and Quinto was handpicked by Leonard Nimoy to play the new incarnation of Spock.
Krall is revealed to have been a MACO soldier. He claims to have fought the Xindi. Both were first introduced on the third season of Star Trek: Enterprise (2001). His reference to fighting during the Romulan conflict as well hints at the unused plotline for the series' unfilmed fifth season.
In the previous two movies, there were only subtle references to the prequel series Star Trek: Enterprise (2001), which takes place 112 years prior to Star Trek Beyond (2016). Captain Jonathan Archer was mentioned in Star Trek (2009), and a model of his ship was seen in Star Trek Into Darkness (2013). However, Star Trek Beyond features quite a few substantial connections. Scotty mentions M.A.C.O. (Military Assault Command Operations), which was a military unit in the last two seasons of the series. Krall was a member of the M.A.C.O.s back when he was still Balthazar Edison, before being given the USS Franklin. He mentions the Xindi and Romulan Wars when fighting against James T. Kirk at Yorktown; the Xindi storyline was featured in the third season of the series, and this implies that Edison was one of the M.A.C.O.s on board the Enterprise NX-01, the namesake starship from the series. The Romulan Wars were supposed to be featured in the series' fifth season, before this got canceled. The design and size of the USS Franklin is very close to the Enterprise NX-01, and the uniforms that its crew can be seen wearing on the video look much closer to the blue jumpsuits featured on "Star Trek: Enterprise". Scotty mentions that the transporters on the Franklin were only used for cargo; indeed, the Enterprise NX-01 was the first ship with a transporter system that was cleared for use by living beings, so older ships would not have had those. Like the Enterprise NX-01, the USS Franklin has polarized hull plating instead of deflector shields, as well as phase cannons and conventional torpedoes instead of phasers and photon torpedoes. Lastly, the USS Franklin is mentioned to be a Warp 4 vessel; by the time that Edison became captain of her, the ship must have been older than 10 years, and most starships were at least Warp 5 or higher by then. Being offered an obsolete cargo ship could have added to Edison's feeling of abandonment by the Federation.
Despite being the third movie of the rebooted franchise, this movie marks the second time the Enterprise has been destroyed, rebuilt and christened "NCC-1701-A". The first was Star Trek III: The Search for Spock (1984) where the original 1701 was destroyed and rebuilt with "1701-A" which made its appearance in Star Trek IV: The Voyage Home (1986).
The Enterprise undergoes a "saucer separation" maneuver first introduced on the pilot episode Star Trek: The Next Generation: Encounter at Farpoint (1987). The separated saucer section then crash lands on a planet in a similar fashion to the Enterprise-D in Star Trek: Generations (1994).
When Jaylah turns on the music, Kirk's face lights up to the strains of "Sabotage" by the Beastie Boys and he says "that's a good choice". This is a nod to the Star Trek (2009) reboot when a young delinquent Kirk is driving his stepfather's convertible and runs the car off a cliff during a chase with authorities. The song on the car's radio is "Sabotage".
William Shatner confirmed that he would not be making nor been asked to make a cameo appearance in the film to mark the 50th anniversary of the original series. However, he appears in a photo at the film's ending, together the rest of the original Enterprise crew. The group photo belongs to Star Trek V: The Final Frontier (1989), that coincidentally was directed by William Shatner.
In the ending scene at Kirk's birthday party, they toast to "absent friends", referring to all the crew members who had died during the mission, and a reference to the same toast Kirk made in Star Trek III: The Search for Spock (1984). Picard also makes a toast to absent friends in the ending scene of Star Trek: Nemesis (2002).
The music used to defeat the attacking alien ships during the film's climax, "Sabotage" by the Beastie Boys, was first heard in the Star Trek (2009) reboot, with young James T. Kirk (Jimmy Bennett) evading a motorcycle policeman and subsequently hurling his stepfather's antique convertible off a cliff.
When Krall and Kirk are battling at Starbase Yorktown at the film's ending, Edison (Krall) mentions watching millions of people perish in "the Xindi and Romulan wars". This is a reference to the prequel series Star Trek: Enterprise (2001) with Scott Bakula playing the commander of the first Enterprise ever built in canon, beginning in the year 2151. The ship was designated NX-01. Scotty also mentions the MACOs when talking about Edison's past. The MACOs were the military personnel that accompanied the NX-01 crew during the Xindi war. The Romulan war that Edison mentioned was supposed to have taken place on Star Trek: Enterprise, and was even beginning to come to fruition, but the series was cancelled before this could be created. However, canon dictates a war with the Romulans in the mid to late 2100s. However, during this war, information about the Romulans was either lost, or nobody ever got a good look at a Romulan. The reason for this is because, in Star Trek: Balance of Terror (1966), upon encountering the Romulans, the Enterprise crew was astonished to see the resemblance they have to Vulcans.
In this movie, there is a discussion between Scotty and Bones regarding having to beam him and Spock back to an old ship one at a time since the obsolete transporter may have spliced him and Spock together. Bones replied that he hated the prospect of splicing himself with Spock, which was a reference to Star Trek III: The Search for Spock (1984), in which Spock had mind-melded with Bones before sacrificing himself to save the Enterprise.
Spock is looking at the birth and death date of Spock Prime. This lists Spock Prime as Second Officer on the Enterprise and Executive Officer of the Enterprise-A. Spock was Second Officer of the Enterprise only for a brief period during Star Trek: The Motion Picture (1979) when he was outranked by the demoted Decker. Through the original Star Trek (1966) series, Spock served in the dual position of Science Officer and First Officer, and as Captain during Star Trek II: The Wrath of Khan (1982). Spock's position on the Enterprise-A was indeed Executive Officer (equivalent to First Officer) and Science Officer.
The first original series motion picture (excluding The Next Generation) not to show or involve Earth.
The "saucer separation" is not a product of Star Trek: The Next Generation (1987). The idea for separating the saucer section of the Enterprise NCC-1701 was in the noted for the original Star Trek (1966) series and there were plans to use this in an episode which never happened.
The Beastie Boys' "Sabotage" is prominently used in this film and in the two previous movies, it's established that Kirk is a huge fan of the group. In real life, the group were huge Star Trek fans. Their song "Intergalactic" references "a pinch on the neck from Mr. Spock".
After Star Trek III: The Search for Spock (1984) and Star Trek: Generations (1994), this is the third "Star Trek" film to feature the destruction of an Enterprise.
The film's main villains (Krall, Manas and Kalara) were humans but their DNA has been altered by using technology from a planet's indigenous extinct species (similar to the Borg featured on Star Trek: The Next Generation (1987) and Star Trek: Voyager (1995)). This also holds true with the guest star Charles Evans in Star Trek: Charlie X (1966) where an alien race did raise a human but the catch is that his DNA was not altered - he used telekinetic powers provided by the Thasians to help him survive on their homeworld but his powers were too dangerous to allow him to live among other humans.
Near the film's ending when the Franklin is used to stop Krall's ship in the center of Yorktown, Kirk, Uhura, Scotty and Jaylah watch the final log of Captain Balthazar Edison in which he details that only three crew members remain and they found a way to prolong life from alien technology left on the planet. The only other aliens from the planet that are seen are the female alien who leads the Enterprise crew to the planet and is killed when the ship flips on her and Krall's second-in-command who stays behind to fight Jaylah and Kirk while Krall carries out the attack. Later on, the last photos seen of the crew of the Franklin when the missing case is closed is Captain Edison with one female and one male member. These could be the other two aliens who work alongside Krall, using the alien machine to prolong their lives and disfiguring themselves to have a similar appearance to Krall.
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Because of Spock Prime's trip to his own past in the first movie, the pad given to young Spock at the beginning of Star Trek Beyond shows Spock Prime's age at the time of his death as only 33 years old when in fact he was 162 years old.
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The opening scene where there is a visual gag about the relative sizes of the aliens and Kirk is likely a reference to a backstory in the original novel "Hitchhiker's Guide to the Galaxy", where an entire alien fleet is swallowed by a pet dog.
After the Enterprise saucer section has crashed, when Krall's bees are seen swarming across the sky in circling formations, the camera pans across a towering mountain in the background, forming an image highly reminiscent of the cover of 1973 French sci-fi comic book classic "Valérian: Les oiseaux du maitre" (The Birds of the Master) - in which the Master maroons and enslaves several space-travelling races, who as a measly reward for their hard work receive a nutrient called "Klaar". In addition, Yorktown has more than a passing similarity to Point Central of the Valérian series.
There are possible references to the original Star Wars: Episode IV - A New Hope (1977): When Krall is flying his swarm ship through Yorktown with two others flanking him is reminiscent of Darth Vader flying his TIE fighter with two others flanking him while defending the Death Star, and the design of the Yorktown Central Plaza shows similarity to the design of the Death Star itself.

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