WARNING! This post contains SPOILERS for Star Trek Into Darkness.
If you haven't seen the film, don't read this post!
In my review of Star Trek Into Darkness, I alluded to problems with the film's story logic. My friend Steve emailed me to discuss the issue further, and in the course of that discussion I realized the film had two more glaring problems.
Near the end of the film, Kirk dies in the exact same way Spock died in Star Trek II: The Wrath of Khan. In a truly cringe-worthy moment, Spock screams "KHHHAANNNN!" and runs off to have his vengeance, beaming down to chase Khan across San Fransisco. But Doctor McCoy realizes that Khan's genetically engineered blood could be used to revive Kirk. In a bit of hit-you-over-the-head foreshadowing, earlier in the film McCoy injected Khan's blood into a dead tribble. Why? That's never clearly explained. Just as Kirk's cold corpse reaches sickbay, the formerly dead tribble, sensing a dramatic moment, begins to coo, miraculously revived. McCoy calls Spock and says "We need Khan alive! He's Kirk's only chance!"
So instead of killing Khan, Spock and Uhura knock out the bad guy, bring him back to the Enterprise and Kirk is saved.
Earlier in the film, Spock serves as Kirk's conscience, reminding the captain that it is immoral to assassinate suspects, that they must be brought to justice to stand trial. Spock's morals suddenly fly out the window when his best friend is killed, and only when he learns that Khan's blood is useful does he quell his thirst for blood...well, sort of, because he brings Khan back to the ship for a transfusion.
We don't see the medical procedure that saves Kirk. But given that Khan was unconscious when he was beamed to the Enterprise, we're left wondering if McCoy just took the blood right then and there and performed the transfusion without asking. Time was of the essence, after all, and having just tried to kill everyone on the Enterprise it seems unlikely Khan was in a giving mood. This may be why the filmmakers glossed over the actual procedure.
But consider this. Minutes ago, Spock had saved all of Khan's followers. Khan admitted earlier that Kirk seems to have a conscience, so the stage had already been set for what might have been a pretty cool scene: McCoy refuses to perform the procedure without Khan's permission. Spock orders McCoy to wake up Khan. McCoy asks for permission, Khan refuses, Spock notes that he saved all of Khan's friends and further notes that Khan must have had at least some respect for Starfleet and the Federation at some point, having worked for them for months. Khan begrudgingly agrees, saving Kirk. He's still a mass murderer, but at least this way his character gets a tiny bit more nuance and the audience isn't left wondering if their heroes only have ethics and morals when it's convenient.
Would this have messed up the film's pacing? Maybe, but the last third was such a mess that I hardly think yet another scene would have made it significantly worse. At the very least the tradeoff helps cement the point that the filmmakers tried and failed to make with this film - that good people are supposed to do the right thing even when it's hard.