I thought the explanation for how Boomer worked goes perfectly with "Water." In that episode, we see her wake-up soaking wet, and through the episode it's clear that she was up to no good, albeit unconsciously. I sometimes wondered if she basically slept-walked through planting the bombs in the water tank or had moments when she became aware of her true self. This answered that. I took Cavil taking the elephant away in their last scene as him giving her up to her sleeper program. She chose her fate and the original Cylon part was gone. All that was left was the human/sleeper program, which had a lot of trouble adapting to Cylon culture once she downloaded.
I think it was the best Battlestar "episode" in a good long while. The plot was iffy, I agree with most posters there, and there were some odd omissions. I, too, wondered where Tory was and why they didn't include a story about the Olympic Carrier. I wondered why they didn't show Ellen being integrated back into the fleet and if Cavil had a reason for doing so. I thought it would've been better if we saw Three/D'eanna. It also succumbed to feeling like a clip show at times.
But the theme of the whole thing was just amazing: "Love lasts beyond death." It was also very tightly focused on this, and brought a whole lot of themes from the series to light. We see Cavil's plan of hatred fall apart again and again in the face of love. Those Cylons just can't stop letting love get in the way of their plans, from Fleet-Simon to Boomer to Shelly Godfrey to Leoben to Caprica Cavil to the Final Five. Every single plot thread was about this, every single one was a love story, mostly ending in tragedy, because of the one Cylon who refused to give into this. Cavil was the only one who rejected love and a chance at redemption, during in his scenes with the boy.
Ironically enough, Cavil's horrific plan is also fueled by a need to be loved. Everyone else found redemption by giving
it. He could only take, and threw a tantrum when he couldn't get it. He never figured out that to get it he also had to give it.
The plot of this movie isn't the point, and I understand how people could be disappointed in it if all they're focused on is a check list of events the story is supposed to hit. Instead, it's more of a series of interconnected short stories about different Cylons and how love ruins and saves them.