Of course, in-universe we're left with some pretty big questions.
- Who defeated Khan?
- What did Khan really intend to achieve with his flight?
- Did Khan get what he wanted when Kirk marooned him?
- With the whole "incomplete records" thing, how many of the "facts" of Khan were accurate, and how many were distorted?
The episode plays out nicely prima facie
, but the truth about Khan could easily be more complex. On awakening, his first and only question is "How long?". In which circumstances would this really be relevant? A journey intended to achieve a destination would rather call for the question "Where?", not "When?"...
If Khan in fact had no destination in mind, but merely hoped to wait out the opposition to him, then "How long?" would be a highly relevant question. If Kirk says "More than three lifetimes", then Khan is safe, because he has been forgotten. If he says "Oh, I estimate three months", then Khan is screwed, because those who want his head on a platter are still alive and sending out Wiesenthals.
Perhaps Khan just wanted to loop back to Earth after the dust had settled? Or perhaps he bet that his ship would eventually be discovered and he could do exactly what he did in the episode. Evidence for him wanting to settle a distant planet is lacking: we never hear of people in the 1990s knowing where or even whether there would be habitable worlds, and we never see colonizing gear or even a means of landing when we study Khan's ship! Indeed, when Khan does colonize, his equipment is stamped with UFP symbology...