The irony of this episode is that its main revelation is something that most fans have probably already assumed. As such, the impact of the episode might have been lost completely as a result.
That revelation is the contention that Massive Dynamic is not only profiting off the results of the experiments collectively known as The Pattern, but that they are directly behind those experiments. It's certainly not a new thought, since it's a fairly obvious supposition, but the characters weren't quite there yet. This brings Agent Dunham to the same suspicions as much of the audience.
Yet I can't help but notice that this is such an obvious connection. Is this a case of writers underestimating the intelligence of its audience, or exploiting it? If it's easy to assume that Massive Dynamic is behind The Pattern, this early in the season, wouldn't it be a good candidate for a red herring? I have the feeling that this episode is meant to lull the audience into a false sense of security.
I think the more important plot point is Agent Dunham's growing instability. She's becoming obsessive to the point of self-destruction. When Walter Bishop is the one telling you you're going too far, it's time to step back and rethink your boundaries. What this is really saying about Olivia, of course, is that she's normalizing what is on the fringe of normality.
And because it's on the fringe, it's not necessarily within the grasp of Walter Bishop, either. Olivia hasn't figured out yet (despite all the mounting evidence) that Walter can speak resolutely about anything. He's constantly sure about things that are dead wrong. Why assume that he knows the full spectrum of what is and what can be on the frontier of human experience? The frightening thing is that Olivia is crossing into regions of consciousness well outside of Walter's ability to conceive. Sooner or later, that gap is going to be costly (which therefore makes it meaningful).
Another subplot involves Peter. Peter wasn't happy about coming back to Boston, and now we know the reason. It's not hard to see how Peter's unsavory associations might complicate investigations and lives in the future. For now, Peter just gets the ball rolling. It's not as interesting as Olivia's mental escapades or the revelations about Massive Dynamic, but like so many other items in the episode, it points to revelations to come.