The last few episodes since the winter hiatus have left me less than impressed. In some cases, I thought the narrative was a bit too jumpy and disconnected; in others, I felt that certain plot elements were being wasted. In essence, I've been waiting for an episode to pull the various threads together and bring them into focus.
This is that episode.
If my instincts are correct, this was written after the series was given the "back nine", so the writers were probably holding back on introducing what is, essentially, a roadmap to the future of the series. The episode actually presents two distinct possible explanations for everything that has been happening, and both of them would be more than strong enough to sustain the series for quite some time.
The FZT manifesto was apparently written by a younger Walter Bishop, back during his initial Harvard days. Presumably William Bell would have known about it, and perhaps that explains his seeming involvement with The Pattern and Mr. Jones. At any rate, Bishop came to believe that beings from an alternate universe with slightly more advanced technology had begun an incursion on our own universe. (It's also possible that Bell wrote FZT using Bishop's typewriter, but that would be a slight stretch.)
The implication is that The Pattern is the result of experimentation by those other beings (perhaps a species connected to The Observer?), essentially a pilot program for an impending war, and the "fringe science" employed by groups like Massive Dynamic, Bishop, Bell, and the "terrorists" is our own reality's attempt to prepare a defense. Individuals with the latent ability to be trained to fight the apparent enemy are located and tested. This explains both the focus on Olivia and Walter's past comments about Peter.
The genius of this episode is that the basis of the FZT manifesto doesn't have to be "real" at all. It still explains the actions and experiments that have been done thus far, if it turns out that Walter wrote the manifesto during or after his mental collapse. Manifestos have a tendency to accumulate the crazy and fanatical, and I could definitely see Mr. Jones and his acolytes justifying any action as part of their belief.
But it would be far more satisfying if the manifesto was accurate, and if it was knowledge of the impending war that led to Walter's psychotic break. If there really is an enemy from another universe preparing to destroy our own, that would make those trying to control and utilize the technology the "good guys", from a certain point of view. And it's interesting to consider the possibility that Olivia would be forced to tread a fine line between law enforcement and saving the world!
This would also make sense of the lingering presence of Mr. Harris, who has been representing (in a personally vindictive way) the "book". As in, doing things "by the book", which Olivia pretty much has to ignore on a daily basis. It was set up ahead of time to ensure that Olivia would find opposition from her superiors in law enforcement before events pushed her to step more and more out of bounds. As much as I hate Harris, he definitely serves a purpose.
This is an effective episode because it changes the landscape without altering what has come before. If the writers continue along this course, I see no reason why the series couldn't continue into a second season. The real problem will be maintaining patience between now and April.