- There's one brief bit of foreshadowing at the beginning: There's a closeup shot of John's shoes just before he puts them on. Why? So the audience can see there's no scuffs or marks on the shoes at all. John's only pair of shoes had never been worn before.
- Earlier in the movie, Bumstead speaks with Schreber about Murdoch. When the conversation turns to knowing the nature of people, Schreber analyzes Bumstead, saying that Bumstead is a meticulous and lonely man. On the surface, it may seem like Schreber is a good judge of people thanks to his knowledge of psychology. That may very well be true. But if you think about it some more, the real reason why Schreber knows about Bumstead is because Schreber imprinted that personality into Bumstead himself.
- Even with the spoiler-laden narration at the beginning, the movie leaves you a lot of apparent plot holes and unanswered questions until very near the end. As the story plays out and John Murdoch finally learns who these Strangers are and what the nature of their experiments is, you come to realize that what you thought were plot holes are all just natural side effects of their experiments, because with those ghastly syringes of theirs, the Strangers have essentially come up with weaponized Handwavium. Nobody in the city ever thinks to ask a lot of the questions that would reveal their situation, such as what the name of the city is, where it's located (what country on what continent on what planet?) or why there's no rain, no sunshine, and never any aircraft overhead. Presumably, that's because the Strangers purged their memories of such subjects just as they wiped Dr. Schreber's memories of his origins. If anybody does start asking any of those inconvenient questions however, those weaponized Hand Waves of theirs will soon lay all doubts to rest: all the inquisitive complainers will soon have completely different identities and memories, come midnight.
- One of the more interesting changes introduced in the director's cut of the film is the return of Jennifer Connelly's singing during her nightclub appearances, as she was dubbed over by Anita Kelsey for the theatrical release, and Jennifer's vocals are admittedly rather lackluster in comparison. But then you realize: Emma has probably never sung professionally in her life, and just because she has the memories of a lounge singer doesn't automatically give her the talent of one. It's another layer showing that the Strangers are mixing and swapping memories around with no real regard for their subjects.
- It only makes sense for the Strangers to be afraid of sunlight and water, since these two things tend to spoil corpses very quickly.
- The ending:
- So at the end the world is saved, everything is great for humans - until you realize that they are still trapped on a relatively small rock in space. And since they can now freely do what humans do, the place is going to be more crowded than a can of tuna in no time. And then there is the panic that might ensue if people notice that they're, well, living on a tiny rock in space.
- Alternatively, even if John is capable of creating a full fledged planet out of the "Dark City" (and we're given no reason to think he can't), the lives of all the inhabitants are still controlled by the whims of someone else. Though in this case Murdock is obviously a lesser evil than the strangers]].
- It's even darker when you consider that humans were totally dependent upon the Strangers for everything, so when John Murdock eventually dies, there will be no one left to provide them fresh air, food, or water.
- "We use your dead as vessels"...and all that that implies.
- Every time Dr. Schreiber was speaking with the Strangers, or surrounded by the Strangers, he knew he was talking to and watching moving, dead bodies. No wonder he's so frightened by them.
- The Stranger who looks like a child.
- It is not clear what Mr. Hand did to the prostitute before he murdered her. But if he did do anything, she would have been getting molested by a corpse. And, according to Director's Cut, her child would have been watching.
- Regarding the "nature vs nurture" message of the film, the scenes with the desk clerk (of the hotel where John wakes up) are telling. The white clerk had several unique figures of speech: "We keep our books neat and tidy", "cash on the barrel", and "No time off for good behavior". The black clerk, put in place of the white one, repeats the first two phrases like they're his own indicating to us that he now has all the memories that the white clerk had. But when the white clerk reappears as a newspaper vendor, he repeats his prior catch phrase, "No time off for good behavior", suggesting that this little quirk was him and not just a product of memories. Taken with the above-mentioned ending scene, it would suggest that film is saying that man isn't purely nature or nurture, but a mix of both.
- Throughout the movie Dr Schrieber was constantly pushing on John that it was (like The Matrix which used Dark City's sets) ultimately his choice, to make things better in the space experimental city for humanity. But instead of taking them back to Earth which seems to be the only logical motivation for the shrink, notice his look of fear when he realizes that John can choose to do what he wishes, and indeed chooses to indulge his fantasy as his first act as God. Which further showed me another difference between the strangers and humans; the strangers, aside from Mr. Hand, were seemingly incapable of performing an act purely for pleasure. Mr. Hand has chosen to take John Murdock's memories into himself and is shown to descend further and further into obsession. Humans are neither cold logical patterns taken from memory, nor creatures of pure base instinct but instead are a collection of memories that describe their identity as a person. It could be a commentary that in middle ground of the two lies the truth about the human condition.
- Poor Walenski may have known even more than he tells the other characters: he may have had a good idea what the Strangers really are. At least, that would explain why he specifically chose a means of killing himself that was 100% guaranteed not to leave an intact body for them to wear as a shell/costume.