"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.