This is another episode that appears to be stand-alone in nature, but actually has direct ties to the overall mythology when all is said and done. This makes the episode very much like "Inner Child", where the case in question is mostly the story of how Olivia and her team acquire insight and information they would otherwise never uncover.
In this case, it's a collection of small revelations, many of them predictable in the sense that they were well-hinted over the course of the season. The followers of the ZFT Manifesto apparently know that Walter Bishop was the author of their guiding text. I get the distinct feeling that the ZFT terrorists know what happened to Walter and his memory, and they also know, to some extent, how to manipulate Walter (and therefore Peter and Olivia) as a result.
It's also revealed that William Bell is the man behind the ZFT terrorist cell. William Bell was identified early as the probable mastermind behind The Pattern, after all. Even if the situation has complicated somewhat since those early days, it only made sense that Bell would still be in the thick of things, and not in a good way. This is especially true after the previous episode, in which Bell seems to be a lot less sympathetic to "Olive" than Walter.
The main question coming out of this episode is simply this: what possible reason could the ZFT terrorists have for experiments like the one conducted? If this is all about a war against invaders from a parallel universe, it doesn't quite add up. That's the case for most of the experiments conducted by the ZFT cell. The writers have done a good job of letting events unfold in such a way that this question rarely comes to mind, but sooner or later, a more cohesive rationale must emerge.
One drawback of this episode is the subplot involving Olivia's sister and the divorce. While the writers do attempt to make a comparison between Boone's unusual level of sacrifice for his wife and the other relationships being shown, it just isn't that interesting. I fear that Olivia's visiting family will end up being victimized before the season is over. Not because I particularly care about those characters, but rather, because it is all too predictable a plot device.