The answer is that it doesn’t mix well because it’s all retcon. Creator Ronald D. Moore would later admit that, aside from the opening credits, Cylons never had a plan, and Battlestar Galactica: The Series it was a later attempt, coming after the end of the series, to explain what the plan was….even if it never actually happened. Boomer treatment in between The program and Season 1 robbed his story arc of its shock value, and seeing him around the other Important Seven before the fall of the colonies is surprising. As with most of the series, if the Final Five didn’t exist, Boomer’s arc would exist, or The program as canon, it makes more sense.
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