The last half of the final season of Battlestar Galactica started not with a bang, but an existential whimper as the fleet discovered a post-apocalyptic Earth slumbering in nuclear winter. Then Ellen Tigh was unmasked as the fifth final Cylon, and Lt. Gaeta and Tom Zarek got their Mutiny on the Bounty on. And as the smoke cleared and the dust settled in this episode, viewers found themselves staring down a veritable freight train of exposition. The board is set, all the pieces are in place, and we're finally beginning to understand that this all really has happened before.
Ellen Tigh popped out of her resurrection tub on a basestar eighteen months ago and immediately began chewing up scenery with Cavil. Apparently, she's something of a mother figure to the Cylons. As in, their architect and Eve. Cavil rages to her about the constricting organic body he's been cursed with, and in the exchange we learn why he's hell bent on exterminating the human race: pure revenge fantasy, brought on by his imperfect emotions. Humans made the "centurion side of the family" to be their slaves, and he won't stop until he's had his (probably pyrrhic) chance at forcing them to atone.
Cut to a delusional Sam Anders, surrounded by his fellow final five Cylons plus Starbuck, and still reeling from the bullet to the brainpan he took last episode. A torrent of prophetic messages escape from his ephasic head, and the disparate strings we've seen over the last four seasons begin to form a coherent whole. The final five were part of the faction of the cylon race who fled to Earth and became the thirteenth tribe. Specifically, they were the ones who researched resurrection and organic bodies for the Cylons.
Safely insulated from the growing rift between man and machine on the other side of the galaxy, they labored to instill the idea of the "one true God" to give themselves a purpose. The final five realized that like their human progenitors, they would probably end up destroying each other, so they set out on a slower-than-light ship to warn the twelve colonies. Unfortunately, by the time they got there the first Cylon war had already taken place, so they seeded themselves among the humans for reasons not yet revealed.
With the destruction of the resurrection hub, the Cylons are facing
extinction. Cavil is desperate for a way to reconstruct the technology,
and he's willing to cut Ellen's brain open to find their old laboratory
on Kobol. Kobol, we now know, is the birthplace of the Cylons, and the
only place they can dredge up the necessary knowledge. Cavil originally boxed the final five for their potentially subversive influence, but there was ANOTHER skinjob
Cylon named Daniel. He was created by Ellen for a special purpose, but
Cavil corrupted his growing tanks and the line was, ahem, discontinued. Facing a hostile surgeon, Ellen
confides in one of the Sharons that her greatest gift to the Cylons was
free will. Perhaps to return the favor, Sharon helps her escape from
the basestar.
John Hodgman (aka the PC dude from those Mac commercials)
makes a fantastic guest appearance as Anders' sardonic surgeon who deadpans all the way through his stint in Cottle's infirmy.
We also get to see Apollo and Roslin deal with the murder of the
Quorum, and the rumblings of a new political order. Once again, Lee
Adama enters the political arena, this time to take over for Roslin, who will govern in name only.
A golf clap (or is that "so say we all"?) is in order for the computer graphics crew at Zoic - they've come a long way since Firefly.
The outsized images of the battle-scarred Galactica we've seen this
season perfectly illustrate the sheer ragtag desperation of a ship held
together by grit and shoestring.
Of course, since this episode seemed to be on an entropy kick, all those scars mirror the fact that Galactica is falling the hell apart. The ominous crack in the hull we saw at the end of last episode has morphed into hairline fractures throughout the ship, and Galactica is about to fold in on itself. Tyrol thinks he's found a panacea in the organic metal the Cylons use on their basestars, but he warns Adama (FORESHADOWING) not to use the jump drive until he can get it fixed. Adama is reluctant at first, but one bottle of space-whiskey, a couple pills, and a look at his dilapidated quarters later, and he gives Tyrol the green light.
Anders emerges from surgery alive, but brain dead. There may be no more ciphers or prophecies for a while, but we've already got quite a bit to chew on. The show's FTL drives are burning white-hot for these last six episodes, and we are careening towards the resolution of the cyclical prophecy that has haunted the human survivors since the first nukes hit Caprica. Battlestar Galactica has always had a clear delineation between "character" and "plot/mythology"-centric episodes, but this was one of the few that managed to do both, and do it well. Episodes like these have happened before, and if this show's past quality is any indicator, they'll happen again.

We do know why they were put onto the 12 Colonies, Cavil killed the five and turned them in to sleeper like agents. This was to force them to feel human to make them see the human flaws that the final five had given the human cylons and make them repent for it. Cavil wanted the five to want to be machines not like humans.
Just as a correction, Zoic stopped producing the effects for BSG some time ago (I think in season 2). Most of the work is now done in-house, with Atmosphere VFX doing the rest. But you're right in that whoever is doing the work is doing an exceptional job. The Centurion in the beginning looked amazing.
I do have to say that this may be one of, if not the best episode of Battlestar Galatica. As the show winds down they are really doing and excellent job of wrapping up all the lose ends. This episode really answers a lot of the questions in Cylon Psychology. Very interesting and very well done.
And how about the Helen as God telling John that he's not a mistake, that she loves him because he created him and offering him forgiveness (which he scoffs at)? One of the things I've loved about BSG is the way that it has explored religion--from fanaticism to the tenets of mercy and grace. And who could have seen Helen as the show's most pure force for good? Excellent episode. And kudos to both John Hodgman and whoever cast him in that role.