Screenwriters Roberto Orci and Alex Kurtzman explained that the dilemma for the sequel was whether to pit the crew against another villain, or to have an "exploration sci-fi plot where the unknown and nature itself is somehow an adversary," like in Star Trek.
According to J.J. Abrams, the time travel-alternate reality concept used in the previous film was a deliberate ploy to enable a reboot for new sagas/films: "The idea, now that we are in an independent timeline, allows us to use any of the ingredients from the past - or come up with brand-new ones - to make potential stories."
Paramount Pictures requested director J.J. Abrams to make the film in 3D. However, Abrams wanted to shoot the movie two dimensionally on film using IMAX cameras. The two compromised, and as a result this film marks the first time in cinema history that a movie was filmed in the IMAX format and then converted into 3D in post production.
Michael Dorn, who had played the Klingon Starfleet Lieutenant Worf, was contacted for a role during the start of filming, and was asked to play an officer. Eventually the filmmakers decided that "they didn't want to mix the old with the new" and cut him out.
According to writer Damon Lindelof, the story began with deciding whether Khan Noonien Singh would be the villain, and they weighed the pros and cons of him appearing. J.J. Abrams felt it would be "be fun to hear what Alex and Bob are thinking about Khan. The fun of this timeline is arguing that different stories, with the same characters, could be equally if not more compelling than what's been told before. Certain people are destined to cross paths and come together, and Khan is out there... even if he doesn't have the same issues."
Both Bruce Greenwood and Peter Weller have voiced the part of DC Comics hero Bruce Wayne/Batman: Greenwood in Batman: Under the Red Hood (2010) and "Young Justice" (2010) and Weller in Batman: The Dark Knight Returns (2012).
The collection of models on Admiral Marcus' (Peter Weller) desk resembles the gallery of old ships called "Enterprise" as seen in Star Trek: The Motion Picture. Both include the NASA space shuttle and the "XCV 330 USS Enterprise" (the ship with the rings around its hull). The models also features the NX-01 Enterprise from the TV show Star Trek: Enterprise. It also features Zefram Cochrane's first Warp ship the Phoenix from Star Trek First Contact (1996)_. The last model is the U.S.S. Vengeance .
On Admiral Marcus' (Peter Weller) desk a model of The Phoenix can be seen. This was the first ship to reach warp drive which was created and piloted by Zefram Cochran (James Cromwell) in Star Trek: First Contact.
The film is dedicated to post-9/11 veterans. This is due to director J.J. Abrams' connection to The Mission Continues, a nonprofit organization that serves as a framework for United States military veterans to do community service work when they return home from overseas. The organization's founder and CEO Eric Greitens makes a cameo appearance alongside other veterans at the end of the film as one of the flag folders. A section of the film's official website is dedicated to The Mission Continues.