One of the prime theories I advance in my backstory is the idea that everybody in the show is a Cylon, which is to say an artificial being, rather than a natural Earth human. That the colonials are AIs programmed to think they are human. This idea is not directly supported in the show, but there are a few items which point to it. In addition it's a very interesting idea.

The most compelling clue within the show is the tremendous similarity between the Cylons and the "humans." They are way too similar, particularly the final five. So similar that the humans can't tell the difference with microscopes or medical scanners. In theory Baltar's scanner can spot the difference in 11 hours, but we don't learn much more about that. They are similar enough to interbreed, something that is used as part of the definition, in biology, of being closely related. Yet even though medical scanners can't tell the difference, the Cylons have an FTL transmitter that can send out the contents of their mind when they die, and fiber optic interfaces in their arms. They can communicate at high data rates with their ships by touching an underwater interface. They have superior strength and resistance to radiation but are more subject to certain kinds. They can receive VR "projections" directly into their minds.

These differences are just too much to be undetectable to advanced medical equipment. A far simpler explanation is that there simply is no major difference -- all the players are Cylons. The "humans" however have never seen anything else, and also may have programming which blinds them to the artificial elements of their own nature. It's also clear within the show that creatures who are not Cylons get external visions and even seem to possibly receive the "projection" the Cylons talk about. In the real world, there are no telepaths or oracles. These things could have a supernatural explanation, but I prefer to view the show through a hard SF lens, and that means that the ability of Roslin, the Oracles, Baltar and Starbuck to receive external visions has some non-supernatural mechanism. They aren't all "Cylons" but some other power exists.

Starbuck also died and was reborn. Some feel this makes her assuredly the last member of the final five. That's possible, but clues point strongly in other directions. If she's not, she still appears to have downloaded her mind. And many wonder how Baltar survived the nuclear attack on his house, which killed Six's body as she shielded him and demolished the building, with just a few scratches. Did he also die and download?

The story of advanced beings who create a race, and then provide a means for their minds or souls to survive death is of course central to many religions but also to much SF. The original BSG series featured an advanced alien race known as Beings of Light who had been manipulating both humanity and the Cylons since the start, and who seemed able to resurrect humans. This would put a hard-SF spin on the more mystical concept of the old series. It could mean all the billions who died in the war were still downloaded (though perhaps just into storage rather than new bodies.)

Because I am pretty convinced the show takes place in the future, I envision this concept as the result of a schism between post-humans who wanted to become pure AIs, and those who wanted to maintain flesh bodies. This idea has appeared in many recent SF novels. It is often the case the new flesh bodies are created and uploaded or AI based post-humans transfer into them to live in the flesh once again. Even the idea of making the new bodies forget their origin to live as humans once did is not new.

Another popular theme both from religion and SF is incarnation. In this case, advanced, even godlike beings, put a part of their minds (small enough to fit) into a flesh body and brain. They live as flesh, and then later re-merge with their whole self. I suspect the "Lords of Kobol" were advanced post-human beings. Some of them may have taken on flesh bodies to live among the simpler folk, and the Cylon's god could be one of them. Several of the characters in the show may be incarnations of larger beings. When Leoben meets Starback, he tells her that their meeting had taken place many times, sometimes with the roles reversed, suggesting reincarnation plays some role in the show, and again that's only possible in a hard SF sense if the beings are already digital, artificial beings capable of reincarnation like the Cylons.