It's often the case that "episode by committee" results in a lackluster, scattershot final product. This is particularly the case when the episode is designed to bring a series to a relative conclusion, wrapping up several plot arcs with as much efficiency as possible. The final script may be the sum of the contributions of the entire writers' room, but having a strong and deft hand bring it together can be a godsend.
That was the case with the previous episode, in which Tim Minear managed to take an over-stuffed hour and make it work, despite several flashbacks and plenty of twists. This episode was short on the revelations by comparison. And that was a major problem, because this was the episode that had to make complete sense of Boyd's motivations, given the reveal that he was the secret co-founder of Rossum (and not Clyde 2.0, as I had mistakenly believed). The integrity of the entire series comes down to making that work.
Based on this episode, the logic is fleeting. Here is how I interpret the direct and indirect aspects of the story:
The founders of Rossum developed the Dollhouse technology, but Clyde quickly came to the conclusion that the technology would get out of control and lead to the destruction of civilization. Rather than destroy the technology, as Clyde would have preferred, the founder and Clyde 2.0 chose to accept the fact that the genie was out of the bottle and develop a covert program to find a way to survive the apocalypse of their own making.
Using their massive healthcare infrastructure, they selected candidates for their Dollhouses that had the potential for a natural immunity to the technology. They also hired technical experts who could take the technology to the tipping point, in the hopes that those same individuals would then have the knowledge and experience to develop a defense. Eventually, an anti-Rossum activist named Caroline came to the attention of the founders, and it just so happened that her biochemistry was perfect for development of a "vaccine" against the wiping technology.
Thus"Boyd" contrived to get himself placed as a handler in a local Dollhouse, ensured that Caroline became a Doll, and cultivated the eventual development of the Echo persona because it was a direct consequence of her natural anti-wiping immunity. While other Dolls had limited success in demonstrating resistance to full wipes, especially Alpha, Echo was unique in how her underlying personality as Caroline managed to serve as a foundation for the Echo persona.
In the process, 'Boyd' came to feel that Adele, Topher, and Echo were all worthy of surviving the coming fall of civilization, and designed the 'resistance scenario' to push Echo to full realization. The final endgame was to eliminate anyone not meant to survive who could interfere in the survival plan. Unfortunately for"Boyd' and his partner, their little plan didn't account for the free will of the individuals in question, and they brought about their own destruction.
Ironically, what seems like a victory is actually the catalyst for the events seen in "Epitaph One". In a way, 'Boyd" was correct; being the source of the tech also gave them the knowledge base to counter the tech when the time came. Knowing the end was coming, their plan was reasonable enough; it was just tainted with massive self-interest. But Team Echo's elimination of the founders (at least"Boyd", and presumably Clyde 2.0 in the creation of the Whiskey seen in "Epitaph One") only makes it that much easier for someone to steal and abuse the tech, and ensures that it will take that much longer to produce a solution without the Rossum infrastructure to facilitate it.
Clearly, if this is an accurate summary of the overarching story of Dollhouse, there is a terrific irony to it. Rossum's founders, despite their self-interested brand of ethics, could be seen as semi-heroic, since they are trying to find a solution to a mess they created. By creating Echo, they are partly responsible for whatever she does in the future, good or bad. It definitely makes one think about the relativity of good and evil.
But that scope was also not part of the show's original DNA, especially given that Boyd's true identity was only conceived in the early planning stages of the second season. Joss and the writers were in a constant battle with FOX over the direction of the series, and it's well documented that FOX was the one that pushed the whole Rossum conspiracy angle. Once something of that scope was shoe-horned into the series, it was a question of having the time and space to explore it properly.
As much as "Epitaph One" gave the writers a punch list of plot and character points to achieve by the end of the second, they had to take a roughly five-season plan and condense it into a total of perhaps 10 episodes, once they knew the writing was on the wall. It's shocking how strong most of those episodes were, given what had to be covered. The "Boyd' scenario may have facilitated that compression, but it also doesn't quite feel like the writers could make it all fit together. Too much of the overarching story is based on conjecture.
As a result, despite the relative resolution, the episode feels a bit incomplete. The cast does its best to make it all work, but many of the twists and turns don't feel earned. To be fair, there just wasn't time to earn each and every payoff, but this is where the decision to include the "Boyd" twist may have been a mistake. It introduced a major complication at the very end of the story, and there just wasn't any time to explore the ramifications properly.
There is still one episode left, so it's possible that "Epitaph Two" will provide enough perspective to smooth over some of the gaps. But it may be that this was the best solution the writers could conceive with the time they had left. If so, they deserve credit for doing everything possible to make Dollhouse a relatively complete story, but the cost was an episode that just doesn't quite work.