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In the previous two films, there were only subtle references to the prequel series Star Trek: Enterprise (2001), which takes place one hundred twelve years before 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, this film features quite a few substantial connections. Scotty mentions MACO (Military Assault Command Operations), which was a military unit in the last two seasons of the series. Krall was a member of the MACOs back when he was still Balthazar Edison, before being given the U.S.S. 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 MACOs 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 it got cancelled. The design and size of the U.S.S. 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 U.S.S. 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 U.S.S. Franklin is mentioned to be a Warp 4 vessel. By the time Edison became her captain, the ship must have been older than ten 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.
After production on the film was completed, and a month before the release, Anton Yelchin died in a freak vehicle accident at age 27. During the ending credits, there is a dedication that reads, "For Anton." J.J. Abrams announced that Chekov would not be recast, "I would say you can't replace him. There will be no new casting. I can't imagine that, and I think Anton deserves better."
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."
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 Star Trek (1966), before this was changed to "Enterprise".
The reference about the rumor that the U.S.S. Franklin might have been captured by "some green space hand" is a reference to the episode Who Mourns for Adonais? (1967).
When Captain James T. Kirk and crew first enter Yorktown's reception area, an announcement can be heard over the intercom referring to a starship with the registry number NCC-2893 just arriving. This is a reference to the U.S.S. Stargazer (NCC-2893), the first ship that Captain Jean-Luc Picard commanded on Star Trek: The Next Generation (1987).
Fiona Vroom: The title guest star of Lolani (2014) appears as an Orion crew member during the Captain's Log scene near the film's beginning.
Carlo Ancelotti: The legendary football manager appears for a minor cameo in this film, he plays a scientist walking out a door on the Enterprise. In a Sky Sports interview, he explained he has a good relationship with the family of Zoe Saldana, so when he was offered the role, being a huge fan since childhood, he couldn't refuse.