Dark City/WMG

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.

• God doesn't create water in the Bible. Water was always there, just like God...

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.

• • Then 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.