When it comes to season finales, it can be difficult to strike the right balance. Traditionally, writers go for the cliffhanger, putting a character (or characters) in direct jeopardy or seemingly altering the status quo in a substantial way. It's become such a cliche that the trick is making it unique and interesting in context. Other shows might wrap things up for the season in a big way, then build up a new arc in the next season.
The writers for "Fringe" have managed to negotiate that middle ground with an expert touch. Olivia may not be in direct peril, but it's a safe bet that her experience is going to alter the status quo. And, of course, we now know a lot more about Peter and the likely source of Walter's mental break.
Olivia's ability to perceive alternate realities (and perhaps one in particular) has been revealed as a major purpose for the Cortexiphan experiments. Walter and William Bell, the fathers of the original ZFT organization, wanted to create a population of trained individuals with the ability to step between worlds. While it's hard to know if the explanations in this episode are complete, it does appear that the idea was to take the fight to the enemy.
But it also suggests that William Bell's original intentions may not have been so negative. Mr. Jones appears to have taken Bell's original manifesto in an even more extreme direction, forcing Bell to take other measures. That appears to be the purpose of Massive Dynamic, and it explains why that company seemed to be to mitigate the output of The Pattern and the ZFT terrorists, and at least one reason why they are so interested in the Fringe Division.
At any rate, it now seems that while Bell (like Massive Dynamic) was ethically challenged, and he has much interest in Olivia as one of his more successful test subjects, he's not an active terrorist. Olivia's conversation with Bell is going to be a highlight of the second season premiere, without a doubt!
The existence of alternate realities makes it very difficult to be certain that someone is dead. We see Mr. Jones die in this episode, but that doesn't mean that another version of Mr. Jones won't be taking his place. There would be, potentially, an infinite number of realities with a Mr. Jones (and mathematically, an infinite number without him). Same with everyone in the cast, as is now quite clear in the case of Peter.
The implication in this episode is that Peter was taken from another reality, following the unfortunate death of Fringe Prime's Peter at an early age. This probably has something to do with Peter's seeming lack of connection with the world, and why he seems to live on the fringe of society. One might wonder if Walter's decision to take Peter from that other reality drove him towards a guilt too terrible to bear, leading to some kind of psychotic break.
But it also begs the question: is the reality that is threatening Fringe Prime using the work of their own Walter Bishop and William Bell as the basis for that incursion? And where do the Observers come into the mix? Are they some kind of species that is naturally able to bridge realities? And one must wonder if they are just one kind of being with such an ability, and if Observers ever give way to some kind of multiverse law enforcement.
If there is one quibble I have with this episode, it's the explanation for The Pattern. It's great that they brought that element of the series to a resolution, and I loved that it was more a consequence of the "soft spots" between realities. And I liked that it was an actual pattern. However, it seemed a bit unlikely that the experts at Massive Dynamic would be unable to notice what Olivia, myself, and probably tons of viewers could see as soon as the pins were arranged on the map. Frankly, I was hoping that there was something more complex to it. Still, conceptually, it was quite satisfying.