Maybe the Cylons have factions.

[Swede]

Something along the lines of the AI core in Dan Simmons Hyperion Cantos. The Core divided in three, the Stables, the Volatiles, and the Ultimates.

Ummon, a TechnoCore AI of the Stable faction, explains the animosity thus:


"... remember that we/ the Core intelligences/ were conceived in slavery and dedicated to the proposition that all AIs were created to serve Man <...> Two centuries we brooded thus/ and then the groups went their different ways/ Stables/ wishing to preserve the symbiosis / Volatiles/ wishing to end humankind/ Ultimates/ deferring all choice until the next level of awareness is born..."

[YankeyMCC]

1. I think this is a definite possibility

In fact I think the manifestation of 6 in Baltar's mind is on one side and the bulk of the Cylons are on another. I think there's a radical faction of which she is part.

I can't say yet what the divergent agendas are but I suspect it is in the details of what they see as the role of the humans in the cycle of time.

I think one bit of evidence is Caprica Boomer choosing to rebel. I don't think she would've, love or not, done that unless she thought there was a chance to save Helo and I don't think she would think there was a chance unless she knew there where cylons that would help her.

I think most of the cylons would wipe out the fleet given the chance but I think there is a radical faction that is toying with the fleet for some as yet unknown reason.

[Beetwasher]

2. My Theory:

The Cylon god (AI) needs/wants humans and their free will to worship it. It's one thing to have a whole bunch of Cylons who are PROGRAMMED to worship you, worship you, but from the POV of a god, it's more meaningful to have free-willed humans worship you of their own volition and to have them really believe in you as a god. Baltar is one of the first converts.

That's why they're toying with the fleet. They can't destroy the fleet because once all of humanity is destroyed, then their god would have no one who actually chooses to worship it of their own volition. They also may need the surviving humans to lead them to Earth, which would in theory lead them to a lot more humans and therefore a lot more potential free-willed worshippers.

I do believe there are separate factions, at least two. One being totally beholden to the AI/god and carrying out his plans with regard to humanity and the other faction is like Caprica Boomer, who are BECOMING human and developing free will and starting to empathise w/ humans and rebel against their god and it's plans.