@Mephistopheles phil,
There's two philosophies in BSG at odds with each other: the Cylon religion, and the Colonial religion. The Cylons, though machines, have developed a sense of monotheism, while the Colonials have stuck to polytheism. Agents for each philosophy aren't quite strict on what side they support, and often have changing priorities leading them to support one side or switch to the other, regardless of their species.
The Cylon religion, as far as I remember, is introduced in the miniseries as being the first of the two religions to be compounded on. Adama meets Leoben at Ragnar Anchorage, and as Adama unwittingly becomes stuck with Leoben for a time, Leoben begins to make philosophical and metaphysical statements, talking about God in the singular. He tells Adama something along the lines of: "[humans] repaid God's gift of a soul with hate, with crime, and sin. So maybe God created the Cylon. Maybe the Cylon is God's retribution for our many sins."
The Cylons see themselves as humanity's children, but in order to come into their own, they tend to blow up ships in suicide bombings and assassinate to achieve their aims. The Cylons can resurrect themselves, because they're sophisticated computer programming. When a Cylon humanoid model dies, its program transmits to a resurrection ship or facility where a new identical body is used to store the consciousness of the dead Cylon. In this way, they live forever.
When the second Leoben is discovered in the fleet, he claims to have planted a nuke somewhere on a ship in the fleet, thus prompting interrogation. During interrogation, he says things like: "I am more than you could ever imagine. I am God. That's funny, isn't it? We're all God, all of us. I see the love that binds all living things together. ... To know the face of God is to know madness. I see the universe. I see the patterns. I see the foreshadowing that precedes every moment of every day. It's all there, I see it and you don't. ... All of this has happened before, and all of it will happen again. You kneel before your Gods and ask for guidance and you can't see that your destinies have already been written. Each of us plays a role, each time a different role. The players change; the story remains the same." Yet, the model Six, Sharon, Doral, and Biers are strict monotheists who believe in a separate God, not a pantheistic God as Leoben believes. In this way, there are differing interpretations of the one true God within Cylon society. One model, Cavil, is actually an atheist who continually berates the others for being religious. Before Leoben II knows he will be airlocked, he reveals a fear of death, a fear his soul won't reach God.
The show is an allegory in some ways of the struggle between Catholicism and paganism in Europe after the rise of Christianity in the Roman Empire. The Cylons, representing monotheism, have attacked and sent the humans, pagans, on the run. Later as the show goes on, the Cylons seem to change their priorities; instead of eliminating humanity, they wish to enlighten the humans with the knowledge and salvation of the one true God.
Dr Gaius Baltar begins the show as the man who indirectly helped the first Six break Colonial defenses and allow the Holocaust. In a display of superb acting, he watches with absolute confusion and panic from his luxury home as the surrounding environment is nuked from afar. Six sacrifices her life to protect Baltar, but that in itself is a topic of debate. The shockwave of a nuke was approaching, she told Baltar to get down, and later in the miniseries, Baltar is virtually uninjured. How can a mere humanoid shield someone from radiation and fallout?
It gets really interesting because when Baltar is chosen among a select few to be evacuated from Caprica, he sees Six smiling amongst the crowd of angry abandoned people; she's not really real, or is she? She reveals herself visibly and interactively to him later on, most of the time with two agendas: giving Baltar prescient information that a hallucination couldn't give someone in order to save the fleet from destruction numerous times, and to convert Baltar to the Cylon religion.
Just who is she? She claims to be a computer chip in his head, but as time goes on, he takes a brain scan, and there's absolutey no chip in his head. Thinking he's insane now, he realizes he can't be mad, because the things Head Six have told him over time were completely prescient and absolutely bizzare. We have the case of Head Six insisting he convert, he makes a joke, and she disappears from his head and fantasies entirely for a time as an identical model of Six named Shelly Godfrey appears in the fleet
in the flesh, no one knowing she is a Cylon, with information that Baltar betrayed the Colonies. As Baltar is close to being executed for his crimes in the court of public opinion, he confesses his sins to the Cylon God, and prays for forgiveness. Head Six returns to his head, and Godfrey mysteriously vanishes, but her glasses are found onboard Galactica, posing the question of who was she and where did she go. As he realizes he is not insane, he asks Head Six who she is. Her answer, chilling, is: "I am an angel sent from God... I am here to lead you to the end of the human race."
We have the Colonial religion, which is based on a Greek assortment of 12 gods. Thousands of years ago, humanity and the Lords of Kobol (the gods) lived in harmony, until mankind fell from grace and was exiled. The Cylons don't even dispute this story. They believe in the scriptures of mankind, albeit with a monotheistic interpretation. They believe the Lords of Kobol did exist, but were not really gods because there can only be one God to them. The humans separated into 13 tribes, 12 clustering to form the Colonies, while the 13th went off to colonize Earth.
The Colonials are guided by the president, Roslin, who has taken a following to the scriptures, the scriptures being just as prescient as Head Six in helping mankind on their journey to find Earth.
But back to Head Six. It's still a mystery who or what she is. She claims to be an angel from God... and in some cases, hints she may be the Cylon God himself. Since TV viewers are used to shows which are logical and not supernaturally inclined (the Outer Limits or the X-files are supernatural, but never has either show had story arcs of angels from God...), most people assume there's a logical explanation, a simple explanation, or even a rational explanation as to who Head Six really is.
I think it's been made clear that something strange is going on in the world of BSG. In their world, there is a supernatural. There are true scriptures, and there is a God, gods, or both. In BSG, mankind was created, not evolved. Creationism exists in BSG. It's been suggested by Baltar's actor that Head Six is a being from another universe, but that doesn't fit the tradition of spirituality throughout the show (the show's lead producer is atheist, the guy who came up with this stuff). In my opinion, Head Six, representing the Cylon God, is either God himself, or a demon sent from God. A demon, you ask? She has displayed violent behavior towards Baltar, abandoned Baltar to teach him a lesson, almost had him executed, and at times, is verbally and mentally abusive.
That's only if Baltar is not revealed to be the final Cylon humanoid model. The Six who sacrificed herself to save Baltar in his house has been resurrected later in the show, and sees Head Baltar. Head Baltar is constantly trying to soothe her conscience about being the key instrument in the destruction of the Colonies.
So if a Cylon sees Baltar, and is a robot, shouldn't Baltar, who sees Six, be a Cylon also? That would make most logical sense, but I have a feeling Baltar won't be the final model. If so, and if the show doesn't reveal what she truly is, I'll be a very pissed off person.
So if that's who she is, what's her purpose? Leoben has told Starbuck she will lead mankind to Earth, and that she have some sort of shared or similar destiny. As the show goes on, a hybrid between Sharon and Helo is born, and Head Six tells Baltar it is
his and her baby. The Cylons are excited the hybrid baby exists; they seem to know something we don't know. Obviously, something to do with the merging of man and machine is part of the destiny of Galactica.
There's more to come, but I'll leave it here for now.