Battlestar Galactica is a TV show and therefore isn’t subject to rigorous scientific analysis. It is full of clues that have multiple meanings which allows the writers more freedom to change the direction without creating inconsistancies in the storyline. Trying to work out what is going on is like trying to escape from a maze that is being continually built, with paths that were previously left intentionally open being blocked off as the story progresses.
What does it mean to be ‘cylon’?
David Eick- I think the audience has to start by asking the question, “What really defines a Cylon?” That’s part of what Season 4 is really going to be dedicated to. And the tip of that iceberg will be introduced in the season finale. (source: TV Guide)
There is no official definition of the term cylon for the reimagined BSG. This article assumes that the term ‘cylon’ means immortal being. As you will see, this one simple assumption opens up a whole new way of looking at the mysteries behind the show.
What is the nature of the Final Five?
RDM - 3/26/2007 …The conceptual framework in which these guys are Cylons, it all sort of works once we laid down their individual back stories… [They are all full Cylons] but they are different fundamentally. (Source)
The Final Five are cylons within the conceptual framework of immortality. Outside of that framework they are not cylons. The skinjobs and raiders are also immortal since they have the ability to resurrect. It sort of works.
The Final Five have two components which for the purposes of this article we will separate into the human character (FFh) and the glowing figure in the Opera House (FFg). The FFg inhabits or projects into the FFh from the place between life and death (TPBLAD). This ’activation’ of the FFh, took place when the fleet reached the Ionian Nebula. This is indicated by the scenes at the end of Crossroads Pt II, Tory is physically sick, Anders gets a headache and all four suffer from confusion. They then feel compelled to go to the gym so that their new FFg components can get together, assess the situation and ensure that the activation has worked out as planned.
The FFg choose to inhabit important people in the fleet for obvious reasons. One of the reasons they did this when they did, may have been to protect the colonials at the Ionian Nebula from almost certain destruction by the cylon fleet waiting there - remember it was effectively Anders FFg component that scared the cylon fleet away.
Now how can an FFg inhabit a standard human? There is already a precedent in the show - the head character. Baltar would seem a standard human, yet he seems to have a double consciousness that was installed during the nuclear explosion on Caprica - a similiar type of phenomenon that happened at the Ionian Nebula with the EMP shutting down the fleet. So this leads to the conclusion that the FFg and the head character in Baltar’s mind are the same type of entity. This is supported by Tigh having visions of Ellen. Ellen appears to him “superimposed” over a real character that is stood right in front of him (Caprica.Six) - this is exactly the same phenomenon that happened to Baltar when the raptor crashed on Kobol (Kobols Last Gleaming) and Head.Six appeared “superimposed” over Crashdown as he was helping Baltar out of the burning raptor.
Head characters appear to their host in the image of someone that the host is familiar with in order to make the host more conducive to influence.
This explains Natalie’s quote about the FF being in the fleet and the reason only four heard the tune that compelled them to go to the gym. D’Anna also said only four where in the fleet while Baltar was on the baseship. However it would appear that Head.Six is in the Last Supper pic but I explain this confusing scenario below.
Its also why RDM didn’t need to decide who the four were going to be until late in season 3, the FFh could be anyone he thinks most appropriate at the time…
Tigh was one of the first names tossed out. Tyrol, Anders, and Tory. And they all had reasons why their backstories worked for the Cylons and for what the final four Cylons would be in particular. Tyrol had a connection to Sharon, obviously, had fallen in love with a Cylon. He was drawn towards the Temple on the algae planet. Anders had survived two resistance movements, very mysteriously. He had also fallen for Starbuck who has a specific destiny, the Cylons keep saying. Tory we knew the least about, so she was a bit of a wildcard. Tigh was the most problematic, and Tigh I went back and forth on all the way up to the point where we were shooting the episode and wanted to make sure that we knew what we were doing, and we weren’t blowing something. (Source Crossroads Pt II podcast)
Last Supper Picture 
The Missing Figure. Someone is indeed absent from the table admits Moore: We have not yet revealed the final [unknown] Cylon. Does that mean the people already at the table aren’t the final Cylon? Moore laughs, you ferreted that our pretty slyly. I didn’t really want to give that away. (Source)
This is classic misdirection. You provide a clue that is quite obvious (space for the missing character), then you act disapointed with yourself when someone points it out and at the same time make them think they were clever to notice. “you ferreted that our pretty slyly” I mean c’mon Ron, you leave a big gaping space in the picture then you congratulate me for noticing it! I didn’t really want to give that away - then why say this unless he is wanting you to think he is giving it away!
MR: Just so I understand what I think you told EW for the story that went with the photo, none of the people in that photo is the final Cylon, right?
RDM: Yeah. I said that. I probably shouldn’t have said that [laughs] but I have said that. So, yeah [that is the case, the final Cylon is not any of the people in the photo.
None of the PEOPLE in the Last Supper picture are the final cylon - Head.Six isn't a person. He was quite cagey the way he approached this and then later regretted saying it. Now if you put Tory in the picture who is also missing, then you have all five human FF members there. Natalie is also pointing straight at Head.Six.
The New Generation - "transformation is the goal"
This all points to the FFg being instrumental in instigating "gods new generation". Hera is obviously tied to the head character which inhabits Baltar with Baltar being her guardian and protector. Tigh's new FFg component makes Caprica.Six appear as Ellen in order to get Tigh to love and have sex with her - love seems to be a requirement for the S7 to procreate.
Nicky = Tyrol + Cally, both human so Nicky has no importance in the storyline (here)
Hera = Helo + Sharon, human + S7, first of the new generation
Six's child = Tigh + Six, human + S7, second of the new generation
Hybrid speech
"And the fifth, still in shadow, will claw toward the light, hungering for redemption that will only come in the howl of terrible suffering."
The hybrid is talking about two entities, not just one. The glowing figure that appears as Head.Six is in shadow. It's host, Baltar is hungering for redemption over his guilt in the involvement with destruction of the 12 colonies.
The Lords of Kobol
Pythia talks about the flood, wiped out most of humanity, nobody blames the flood. The flood is a force of nature, through the flood mankind is rejuvenated, born again, I was not the flood you see, I blame myself, I blame myself, that God made the man that made that choice. God made us all perfect. - Baltar, The Hub
The glowing figures in the Opera House are five of the Lords of Kobol. They are the mythical flood, they work behind the scenes and manipulate mankind by appearing as head characters and guiding them periodically through a cycle of destruction and rebirth. All of this has happened before and will happen again...
The original programmers
The head characters aka Lords of Kobol are the original programmers. Once the dumb chrome toaster cylons became self aware, they were able to be inhabited by head characters who then guided them toward creating the S7. This is where they got their resurrection technology from and its also why the Razor hybrid and guardians made a quick escape from the scene before they were 'enslaved'. The S7 were probably created as a new race in their own right but once it was discovered that they couldn't build a model that could procreate, they realized that they still needed the humans to fulfill one of Gods most important commandments.
The Thirteeth Tribe
Adama - "And zeus warned the leaders of the 12 tribes that any return to kobol would exact a price in blood."
Why did Zeus, one of the Lords of Kobol warn only 12 tribes not to return to Kobol when it is stated numerous times that 13 tribes left? Because Zeus is a member of the 13th tribe so he didn't need to warn himself. The Lords of Kobol, the glowing figures in the Opera House, the head characters, the Flood and the leaders of the 13th tribe are all the same thing! The Opera House is what allows them to appear as head characters.
God
"Five pillars of the Temple were fashioned after the five priests devoted to the one whose name [cannot be spoken]“
The five priests being the members of the 13th tribe that 4000 years ago were inhabited by the same five head characters. So the “one whose name cannot be spoken” and Head.Six’s “one true God” are one and the same. His name cannot be spoken because he has no name! In this sense, God isn’t a person, a character or an entity that will make an appearance in the show - its more of an idea just like it is in all religions. The head characters/LOK, whatever they really are still believe in a God, they still question their own existance, their God is the same God as in any monotheistic religion.
D’Anna recognizing the Final Five
Incidently, its interesting that Head.Six tells Baltar he is the one that is supposed to look through the Eye of Jupiter and see the faces of the Final Five. So it seems that Baltar was destined to discover the truth behind Head.Six.
Summary
The FF and the S7 are both cylons “within the conceptual framework” of immortality - as RDM himself says “it sort of works”. The glowing figures in the Opera House are immortal, the cylons have resurrection technology and therefore they both are, in a roundabout way cylons. The glowing figures in the Opera House inhabit both human and cylon and appear as head characters in order to influence their “hosts”. The manifestation of one of these figures appears in the Last Supper picture as Head.Six. Head.Six is an appearance of the final cylon within Baltar’s mind - she isn’t a person. Baltar is no more a cylon than the other four FF members.
The final cylon is one of the glowing figures that appear in the Opera House or Head.Six, depending on how you want to look at it.
Actors reaction to the identity of the final cylon
Sackhoff: You know, at first I was a little disappointed. I was like, “Really? That’s what you’re gonna do? Okay…” But then the more I thought about it, I was like, “Oh… this makes so much sense. That’s fantastic!” And I realized that if the fans do what I did, they’ll be happy. If they take it for what it is on camera, they’ll be like, “Excuse me?!” (Source)
During an interview with Roslin/Six and Starbuck, Six says that you will be compelled to go back and rewatch the show. Can anyone else but Head.Six elicit this type of reaction? (Video Source)
Final notes
This theory doesn’t attempt to explain the origins of the Lords of Kobol. It still works if you assume that the Final Five reincarnate, although not as well. They could also be original cylons created thousands of years ago by humans on Earth. I suspect that this will be an open question and left to the audience to debate for the next 20 years, just like the beings of light in the original Battlestar Galactica.
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