This episode is a mixture of beauty and brutality, and in this instance, both are captivating. After the mess that was the previous episode, I was a bit worried that the writers were going to aim high and shoot low with the ending. This episode, however, makes it look more likely that the series will have a strong finish after all.
First, the beauty. I've always been aware of the role of music in this series, and that definitely helped to enhance my enjoyment of this particular episode. It set a mood of melancholy and foreboding from the very beginning, and it kept me spellbound throughout Kara's emotional and psychological journey.
It doesn't hurt that the essential thrust of the story appears to confirm my suspicion that Kara's father was the recently mentioned "Daniel", perhaps the only surviving Seven. That's not necessarily the only interpretation that could be made, but it is becoming the clear frontrunner. With so little time left, I have reservations at the writers could introduce anything else that wouldn't feel like a deus ex machina solution.
"All Along the Watchtower" provides a musical connective thread between the Final Five, Kara, and Hera. Where the Final Five seem to hear the music more directly, Kara and Hera experience it more subconsciously. For Kara, it comes out through a kind of Cylon projection, summoning up a version of her father to guide her to self-awareness. Hera's not in a position quite yet to explain how she knew the music, but this could explain why Roslin seemed to react to something in "Crossroads".
Presumably, this brings Kara closer to understanding her "special destiny". If her father was one of the skinjobs, then in a very real sense, she co-opts Hera as the first Human/Cylon hybrid within the Colonies. It would explain why Kara has always been searching for her place in the world; there's never been anyone quite like her.
There's still the matter of her resurrection to consider. That it took place on or near Earth appears significant; she didn't resurrect among the Cylon fleet, after all. This implies that Kara was resurrected by the same technology that brought back the Final Five after the annihilation of Earth. The location of that technology could be significant, because as we see in this episode, the fleet has been searching for a suitable planet to inhabit for weeks, and the constant grind is getting to everyone.
The anticipated Human/Cylon alliance is in full swing, with the Cylons now having a seat on the newly reconstructed Quorum (that we haven't actually seen). They're flying missions together, their working to keep Galactica space-worthy together, and they're acting in accord on critical items such as justice and survival. Between the mutiny and the Cylon civil war, neither side has what it needs to make it alone, and they've adjusted accordingly.
Internal to the story, Galactica is still falling apart at the seams, and even before the damage was done by Boomer's escape, it was only going to make it through one more jump. The implication is that this final jump would be to whatever planet they manage to find. Between wrapping up the mysteries surrounding Kara and the particulars surrounding the alliance, that might have been enough on its own to sustain the rest of the series. But there's still the small matter of the external conflict with Cavil.
It makes sense, based on the ease of escape in "No Exit", that Boomer was helping Ellen as part of a plot. Ellen made it clear to Cavil that Hera was the future of her plan, so of course his own success would hinge on controlling (and, logically, eliminating) that asset. Beyond what Boomer did in this episode to convince Tyrol to help her with her mission, using their past history as a pretext, I'm not sure how that was supposed to work.
Cavil couldn't have known that Boomer would have the chance to twist Tyrol's emotions, so the plan was essentially a last-ditch effort. It never should have worked. That makes it a bit of a plot convenience, but it's the kind that works because the audience needed a resolution to the Boomer/Tyrol thread. It also pushes the final confrontation with Tyrol into the short term, which allows it to coincide logically with the Galactica's final days.
There is a certain level of irony here. Athena seduced Helo by posing as Boomer on Caprica during the first season. In a way, Athena co-opted a life that could have been Boomer's. Boomer gets her pound of flesh in this episode, and it is not at all pretty. It's actually one of the more disturbing moments in the entire series run. Boomer beats Athena to a pulp, essentially forces Athena to watch her sleep with Helo, and then steals Athena's daughter.
What makes this so crushing is the realization that Boomer has been a victim for so long that her actions must seem justified in her own mind. Boomer's attempted assassination of Adama was programmed into her (presumably by Cavil). She tried to atone for that mistake in the past, but it always went horribly wrong (particularly the New Caprica experiment, which was clearly undermined by Cavil in retrospect). Boomer ultimately has been used and abused by Cavil in more ways than one can count (including their "affair" on the baseship).
This doesn't excuse Boomer in the slightest, but it does point to the notion that Boomer is still being used; she's still not acting out of her own personal agency. Either that will never change, and Boomer will end up being a tragic figure, or the moment that she takes control of her life will be a critical point of the finale.