No spoilers for future episodes. Everything here pertains to this, and prior episodes.
Another reviewer complained that the original version of this incident took place before Peter joined the Fringe team, so this episode is illogical. This seems to be a good point to clear up the nature of how/why we're seeing the events of this episode, a second time, as this episode is making a point that I think some folks are missing.
When the Observers attempted to erase Peter from the timeline, the initial, more obvious impact of that erasure didn't extend to Peter's involvement with Fringe, it extended to the day Peter drown in the lake, on the day of his kidnapping. This completely altered the state of mind of Walter, his wife, and their entire history, going forward. Walter, already distraught from his own son's death, now had the additional guilt of having brought about the death of yet another version of Peter. We also learn in an earlier episode that Walternate was also aware that his son had drown.
The point is that both Walters had profound influence in each of their universes, based upon their involvement in "world changing" science (discoveries, inventions, etc.), with Walternate even becoming the head of what one could argue is the most powerful entity in his world. Yet, each of their mental states, motivations, , etc., would have been profoundly altered (along with those people around them), from that point forward. One of those people would have included David Robert Jones, certainly resulting in a completely different "future path" for his life, and motivations. (And remember, Peter was the person who killed Jones, in the original timeline, which is why he's still playing a part in both universes, in the current timelines.)
Chaos theory is directly applicable to all of this, such that these changes do not simply impact the core set of people that we know. There would be a massive ripple effect from the day of the drowning, going forward, in both universes, which already accounts for the many differences that we witness. But, the impact also goes backwards in time, and starts much earlier. Remember that Walter built "the machine", and sent pieces of it "back in time", pieces that the lineage of "Sam Weiss" family members discovered, and expended great effort to understand, and eventually document. But in the original timeline, Peter was a key component of that machine, and his erasure would have had an impact on the nature of the machine, and how it came to be understood. Thus, his removal from the timeline would have gone all the way back to when the original Sam Weiss, and his immediate family, discovered the machine, searching for its remaining components, as well as researching/documenting it. And yet again, chaos theory applies, as the ripple effects from that (much, much earlier) change to the timeline, would have the potential for profound changes through all of the subsequent historical timeline.
Bottom line... we see, in some cases, vast differences between what has happened before, and what is happening now, but all of that makes perfect sense, when one considers just how far back the timeline would have been altered, by the removal of just this one key person.
The more interesting discussion (to be having at this point in the series) relates to the conundrum of how Peter's refusal to be erased by the Observers, has started to ripple through, and somehow "unwind", the Observer-imposed timeline (as is evidenced by Olivia's reconstructed memories). But, that's a puzzle for another time.
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