One would expect things to calm down a little after the relentless events of the previous episode, but that's not quite what happens. Instead, the fallout continues, the body count mounts behind the scenes, and the delicate fabric of Colonial society threatens to tear itself to ribbons. More than that, we get a chilling reminder that the heroes of the story are hardly white knights.
Adama is walking around, picking up all the pieces, trying to maintain some sense of order, personal and professional, in the face of crushing loss and despair. Adama also doesn't seem to be doing so well physically; he appears ill. It's impossible to tell if that's just the result of his attempt to contain his psychological and emotional pain or something more medically serious. Whatever the case, Adama is just barely holding things together.
Part of his problem is Roslin's decision to abandon her duties as President. All things being equal, Zarek has every right to step up to the plate and pursue his own agenda in her absence. It's also hard not to see his point of view. Working with the Cylons and trusting in their technology, even when it holds the promise of aiding Humanity's survival, must sound like insanity. After all, as more than one person points out, Humanity wouldn't be fighting for survival if it wasn't for the Cylons in the first place!
All of this harkens back to Adama's initial questions about Humanity's worthiness to survive. Ever since the Cylon attack, Humanity has been at cross-purposes. On the one hand, they continually try to overcome their own worst impulses to fight the enemy and survive another day. On the other, the hope they've held for years now is deliverance. They've been striving to find Earth because, in the minds of many, Earth would have magically solved all their problems.
Of course, even if it had been inhabited by the descendents of ancient Colonists, how could it have lived up to expectation? Unless they were advanced far beyond the fleet's standards, they would have been in rather sudden dire straits. As it stands, Earth had become a symbol for the ultimate external solution to Colonial problems.
Yet isn't that what started this entire problem in the first place? Humanity sought to ease their burdens and externalize tasks and responsibilities onto the Cylons they created, never once thinking that their mechanical servants would turn on them. And this is despite a religious order that knew of prophecies and histories that warned of just such a fate! In a very real sense, the Colonists are best defined by their penchant for passing responsibility for their survival and well-being to others.
Which is why Adama, Roslin, and those following them have been portrayed as the heroes of the story, even though they've been terribly flawed and questionable in their methods. These are the people getting things done when the times require it. They're making the hard sacrifices. As a result, it seems unnecessary, even traitorous, for someone with Zarek's reputation to question their right to represent the fleet.
But the episode goes out of its way to show that Adama doesn't really have anything on Zarek. The man can be a rabble rouser, and he has some questionable connections, but Adama blackmailed him into getting out of the way of progress as Adama defines it. (And there's no question that this is Adama's call, not Roslin's; Roslin seems to be going along with it more than pushing for it). This ties back into the notion that some colonies, like Caprica, were more powerful and entitled than others.
Which, in turn, ties into one reason why permanent alliance with the rebel Cylons would be a rather good move. If Adama is serious about moving on from the disappointment of Earth and finding a new direction and path, then bringing the Cylons into the fold and giving them a voice (perhaps a thirteenth seat on the Quorum?) is the best option. It still won't be a perfect solution, because resentments will linger for generations to come, but all the signs point to the notion that merging the two into one society is the only viable course.
There is another source of pressure, of course, and that would be the child of Tigh and Six. Even as the "importance" of Nicholas is wiped out of the equation with an unexpected paternity switch (shall we drag Cally through the mud some more?), this new child points to two things: a possible future for the Cylons as an evolving species, and the unique nature of the Final Five.
The Colonists would be very wise to forge this alliance before the Cylons come to the odd conclusion that they don't really need the humans at all. Or they need to figure out what makes the Final Five so special, such as the strong possibility that they are the end product of the previous cycle's Human/Cylon genetic merge, ala Hera. And all of this has to come to light before the alliance pulls itself apart.
Fresh off the events of "Face of the Enemy", the webisodes devoted to Gaeta, we see him emerge as the fanatical anti-Cylon warrior under Zarek's tutelage. A lot of people in the fleet are going to be willing to march for that cause, and it is not going to be pretty. Gaeta is essentially plotting a coup, and those are seldom without bloodshed.
The wild card in all of this is the rise of Baltar's cult, still percolating in the background. Given his previous leanings, would he marshal his followers to back Adama's alliance with the Cylons? It seems like a reasonable assumption, but with Baltar, who can say? It would be rather interesting if Adama and Roslin were forced, by circumstance, to ally themselves with Baltar. The way things are going, however, anything seems possible.
One final word: Ron Moore did a bang-up job with the direction of this episode. He avoided the usual pitfall of trying to introduce "trick shots" to prove that he has a unique perspective to show, and his style meshed with what has been prevalent to date. Moore had some great comments to make about the experience on the official podcast, and I would recommend that to those interested. He also mentions that a longer cut of the episode will be on the eventual DVD set; something tells me that will be the case for most of these final episodes.