One minor plot hole in Star Trek Beyond was originally going to be fixed by adding a subtle reference to Star Trek II: The Wrath of Khan. J.J. Abrams's Star Trek reboot is separate from the Prime Universe, with the events of its movies taking place in an alternate timeline known as the Kelvin Timeline. This has allowed for movies that aren't constrained by decades of canon and the restrictions that go along with it, and for the most part, it has allowed for satisfying Star Trek stories that are easily accessible to a wider audience.
However, that doesn't make the movies of Star Trek's Kelvin Timeline impervious to plot holes and inconsistencies. One such issue arises in Star Trek Beyond, wherein a significant character from the previous movie, Star Trek Into Darkness, simply disappears without a trace. None of Star Trek Beyond's characters mention her absence either, making it seem as though the Kelvin Timeline's Carol Marcus has been entirely forgotten between the two movies. Marcus was not only a key character in Star Trek Into Darkness but also in Star Trek II: The Wrath of Khan, in which she is the lead scientist on Project Genesis and the mother of James T. Kirk's only son.
Related: Star Trek Into Darkness' Chekov Trick Is A Perfect TOS Reference
As well as playing Montgomery Scott in the Kelvin Timeline, Simon Pegg co-wrote Star Trek Beyond, and he revealed that there was originally a line in the film's script that referenced Carol Marcus' absence. The line would have drawn a parallel between Star Trek's Kelvin Timeline and the Prime Universe by revealing that Marcus had gone to work on Project Genesis. Had the line been used, it would have not only referenced Wrath of Khan but also would have set up a perfect
Read more on screenrant.com