The world we live in was originally Dark City, and John Murdoch was literally God
What was the very first thing that John Murdoch does? Creates water, and the sun, just like in the Bible.
- Technically, the Bible actually says God created the universe first, though it does mention waters being a part of that universe before anything had any form to it. Then God created light... the sun and stars came later. John Murdoch might have still created our world, though.
Centuries later, everyone in Dark City gained the ability to Tune in different amounts
As they subconsciously expanded their small world, gradually their lost memories of Earth and created new creatures based on popular culture and explained their powers as magic. At some point, the entire flat planet became dependent on Tuning or "belief" and "magic". And later, four elephants and a giant turtle
were created to support the expanded Dark City.
- Or, after expanding the city to a proper size world, they started to specialize their tuning to the point where each of them would be able to affect one of the four classic elements.
John woke up not because of his power, but because the memories are incompatible
At first, the implication seems to be that John's waking up during his imprinting is related to his ability to tune—but it's mentioned that other people have awoken during the midnight tuning, most notably Walenski, and there's no indication that any of them are capable of tuning. It's also mentioned by several characters, not to mention John himself, that he's simply not capable of being the murderer that he was supposed to be. What if he woke up because his mind was rejecting the memories of doing things that he would never do—and the same problem has been occurring sporadically all over the city?
- Someone has been reading his Worthing Chronicles (by Orson Scott Card). The same result happens when they try to put in someone else's memory bubble into the emptied minds of another, or even year's older bubble of the same person's memories.
Emma was originally Marion from Requiem for a Dream
After the events of the film she was abducted by the Strangers and forgot her former life and drug addictions. A hint of this might be the fact that she is seen standing on a peer with John watching (she was doing this in Harry's imagination a few times in RFAD)
As in the body he inhabited was. On their way back to Transylvania after the events of the film, Riff Raff and Magenta end up encountering The Strangers. Things go awry as the alien life-forms clash, and Riff Raff ends up killed in the resulting confrontation. Then the Strangers decide to make use of the available body to give Mr.Hand a vessel. Upon awakening in his new form, Magenta is murdered by what used to be her brother and Mr.Hand takes his place among the ranks. His flares of temper, sadism, disobedience, and awareness of a better existence after the imprint could be remnants of Riff-Raff's personality resurfacing as the hive mind wanes and he gains more freedom and control of himself.
Dark City isn't a physical location, but rather a subsection of the Matrix. It serves as laboratory for the Machines as they refine the Matrix for its prisoners. John Murdoch is The One, or rather a prototype for the One.
Everyone got sunburn.
In the dark for years and then John turns it towards the sun? Ouch.
Almost every movie or tv show you've ever seen has actually been an experiment on Dark City.
Why do you think we keep seeing the same people as different people over and over, and how their lives only take 30 minutes, 1 hour or 2 hours and seem to just fade away in the end and lack any long term consequences.
Dark City evolved into the world of the Matrix.
Realizing that knowing the truth people on the Dark City were going nuts due to the limited size of their environment and knowledge they were in a fake world Murdock created a neural simulation, erased everyone's memories and entered them into the simulation. He created a race of machines to keep the bodies safe, then he entered the simulation himself. This is why they have the belief that there was a man born inside the Matrix who could remake it however he wanted, they were close to correct. However as the experiments of Dark City showed the human soul could not be entirely programmed or controlled, hence they rejected the fake reality and entire crops were lost, until an intuitive program came up with a solution. Outside of the neural simulation Zion is built on the remains of the Dark City, which is why the outside world is so limited in its size from what we've seen.
After John Murdoch got bored with micro-managing Dark City (in about a week), he went looking for home.
While nobody remembers Earth anymore, it's probably not too far away: the Strangers didn't go looking for any more races to populate their city, so it's probably still in our solar system. Once Murdoch took to asking what lay beyond the city, it would be a simple matter for him to make a big observatory telescope and start looking around to see what else might be orbiting this star. Once he found Earth, he kicked the engines into gear and propelled the whole city home. The reason we don't see a sequel detailing this is because this part of the story would actually be pretty boring to watch, as he and the other citizens start finding out all kinds of fascinating things about our world and its solar system that we viewers already know.
The people aboard the city were abducted in the 1950s.
If the city was designed from the memories of those abducted (which is likely), the technology level and aesthetics peg it as being in the 1950s or the very early 60s at the latest.