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Klvino [ORB] said:
Keep in mind the Chief, like everyoen else - but boomer - has lost everyone he or she knows. Discovering your lover might be a cylon after the destruction of your civilization is something a person might block out or even turn a blind eye to.
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I suppose so. But would that be true even if your lover were partly responsible for you losing everyone else you know? And activly trying to finish the job, including killing you?
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The Chief is msot likely realizing that she is one by now, but also fears for his own safety like Baltar feared when he found out Six was a Cylon and the colnies were under attack.
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The difference there was that Baltar knew he would be blamed for the attack. It was his own arrogance and lust that gave the Cylons the information they used to wipe out the colonies. He has to figure that once the truth comes out he'll be spaced, or chained to a wall at best. So his ongoing deceipt is in his own personal self interest. And in his arrogance he probably thinks he'll figure out a way to turn the situation around still. Boomer didn't use her relationship with the Chief to get access to the bLasting caps. Or if she did they didn't make that clear. It seemed she was just using her own access as a member of the crew. So the chief wouldn't be on the hook for anything she did before he found out. But by covering for her now he is definetly screwing himself, and endagering the fleet.
It seems to me like they are setting this up as the Boomer/Cylon on the fleet is malfunctioning or developing a concience or something. Once she's discovered I could see them trying to "reform" her and keep her around as some sort of double agent to use against the Cylons.