Faithful to their habits, the minds behind Fringe followed a major event — impacting our characters emotionally — with a seemingly standalone story having subtle parallels with some elements of the earlier event. Also, by leaving their options regarding the physics of timelines open, they kept us on our toes in a story that put Peter at the center and very successfully built on what we know while developing the beginning of this season's overarching storyline.
In "And Those We've Left Behind," the Fringe Division investigates strange time displacement events, meaning events from the past or future (in this case only the past) bleeding through the present with potentially devastating consequences. The team understands the anomalies are caused by human technology and quickly identifies the source and this is where it becomes interesting for the parallels. The source is a house owned by Raymond and Kate, who have been married for thirty years. Raymond has created a machine based or his wife's works in theoretical physics and has put their house in a time chamber, meaning a bubble where time doesn't flow like on the outside. With the machine, he has been using a past iteration of Kate to complete the equations so that the time distortion is "infinite" and keeps them together in the chamber for more than a few minutes or hours. Love is his motivation, as in the present his wife is very sick.
The previous episode was mainly about how the characters dealt with Peter's appearance in their lives. Interestingly, those who knew him the most in the previous timeline were the most reluctant to accept him. Peter having all his memories from that past timeline faced the coldness of the woman he loved and the unequivocal rejection of his father, while his very appearance seemed to be rooted in the fact that he couldn't let go of them. Like Raymond, Peter remodeled the "present" using a machine. Like Raymond, Peter was operating the machine and kept his memories. Like Raymond, Peter was motivated by love, and like Raymond, Peter ultimately faced some sort or rejection in the new reality he created. Granted, in the case of Peter, it's because they don't remember him while in Raymond's case it's because Kate didn't think living in a bubble was true life, especially given the consequences on the outside.
The story very competently led us through the above, while simultaneously continuing to deal with the fallout of Peter's appearance in the timeline. Walter's refusal to be involved in anything to do with Peter, besides providing a bit of humor, allowed him to see his son in action and soften his resolve, seduced by Peter's brain more than by his unflinching desire to do the right thing, which worked on Olivia instead. Walter having the backseat allowed Peter to take the scientific lead in the investigation like never before, showing to the whole division how much of an asset he could be. In the previous timeline, Peter was mostly used as a scientific assistant and a translator for Walter, rewording many of his unintelligible sentences so that the team members and the audience could keep up. This change is one of the many corrections the show designers are introducing and it is welcome.
Being involved in the case also meant Peter could spend a lot of time with Olivia. She gradually softened a bit after observing him with herself and with others (including the little girl), but most importantly, it allowed her to finally understand his connection to her, and this is where the show is sending a mixed signal or maybe keeping its options open. Until now, the assumption was that history had been rewritten, meaning that the former timeline didn't exist anymore, which is why Peter should have disappeared. The Observers didn't exactly leave room for us to understand what is happening as a parallel timeline.
Olivia, in a manner typical of the character, showed she understood the iteration of herself Peter knew was important to him. He confirmed she was, then added "She is." The way the two characters spoke of Peter's previous life and the way they acknowledged they were strangers to each other mean they believe Peter can actually get back to his Olivia. The problem is that if we (and the show) stick to the initial understanding, Peter getting back to the previous timeline would make this Olivia and her timeline disappear. It will be interesting to see what happens when Peter and Walter start tackling the question.
In addition to keeping doors open on how it will deal with the timeline issue, the show displayed its command of complex storytelling by properly using what the audience has gathered from the past and present timelines. The story showed things from Peter's perspective (opening scene in the park with Olivia). It had Peter casually making references to what he knew about Walter and seeming surprised when things were different ("He [Walter] lives here? Since when?"). Many of those things involved Olivia and participated in convincing her that he didn't have a hidden agenda.
With so many things happening, some characters and some events have to be sacrificed.Astrid is still there, but not as before and even the newcomer Lincoln was pushed aside a little to make room for Peter. Personal favorites during the episode were the time jumps. In a less ambitious show (with a less skilled creative team), they would have been used very differently. Here, they were cast aside by Peter and kept between the audience and himself, providing some humor and helping him understand what was happening. They are likely to be back though, given how Peter's appearance is the event that allowed Raymond's machine to start working, but as always with Fringe, nothing is certain...