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"The End of All Things" might have been the end for September the observer, but it was certainly the beginning of many things as far as the fourth season story arc and to some extent the overall series narrative are concerned. It managed that by tackling long standing questions with some revelations that raised new questions. Heavily steeped in the series mythology, the story somewhat left its options open on the subject of timelines by pushing Peter after what, to me at least, felt like a red herring.
Abducted at the end of the previous episode, Olivia was at the center of the story designed to advance the overall narrative. Right at the beginning, she finds herself locked in a room with Nina Sharp who explains she has been held against her will for several weeks now. Enters David Robert Jones who would like to "activate" Olivia by forcing her to switch on a few lights simply with her mind: it would seem Mr. Jones, even across timelines, is predictable that way. While all this is happening, the Fringe division is holding another Nina Sharp captive, suspicious as they are that she is responsible for dosing Olivia with cortexiphan. They have nothing much to cling on until the wounded September appears in the lab.
It felt as if the whole trip into September's mind had only one purpose: tell Peter he was in the right time, the right place, and had to find a way to make it work with Olivia, who is his Olivia. The coating was nonetheless interesting. We now know the observers are literally from the future, and a personal favorite was how the story used Henry, Peter's son in the previous timeline. Peter had a few seconds to marvel at being a father and face the harsh reality of losing a child. What's even better is how that child was used as one of the reasons why the timeline had to be rewritten.
From Walter's notes dating from the cortexiphan trials, David Robert Jones knew Olivia's ability would be "triggered by sparks of intense emotions." His rationale for abducting the Fringe agent was to activate her in a controlled environment by generating the sparks through torturing his fake Nina Sharp. However, he didn't take into account an unexpected twist, the fact that Olivia's memories from another timeline — he is still not even aware of — would bleed through time and affect her feelings for her adoptive mother, dampening the intensity of her fears for Nina, real or fake. This was extremely well laid out, just as the fact that we have already been through a similar "activation ritual" was integrated into the story and allowed it to move forward instead of feeling like a déjà vu. The fact that there was no waste of time as soon as Peter was threatened and that her actions were much more powerful than whatever we witnessed before further showed this was not just an activation. Having the memories of Olivia from the previous timeline, she is more powerful because what happened here was building on past events.