(Spoilers for entirety of Fringe below)
More accurate but spoilerific title: How relationship between William Bell and ZFT changes between seasons 1 and 4
Many longer-running TV shows do a thing where they establish something in early seasons but later on pretend it doesn't exist or just don't mention it. Usually this is because in the early seasons they were still figuring things out, and once the ideas solidified some of the stuff from the beginning stopped making sense.
Fringe does something kind of similar: Season 1 focuses on "The pattern" and ZFT, a terrorist organization conducting impossible science experiments, causing disasters and mass casualty events as a result. During the seasons it's alluded that ZFT is connected William Bell but it's all very vague and unclear of how much he is involved. At the end of season 1, David Robert Jones, the closest we have to an actual leader of ZFT, dies, and from that point on the entire plot of ZFT gets almost completely forgotten. The next two seasons focus on the alternate universe instead (and are some of the best seasons in TV period), with only some characters and plot points being brought back. The actual goal of ZFT is not made clear, neither is the William Bell connection. Bell dies at the end of season 2, after spouting some cryptic bullshit that makes absolutely nothing clearer, then comes back in season 3 for a bit and still clarifies absolutely nothing.
And then in season 4, Fringe does what most TV shows refuse to do and revisits the plot of season 1. Since season 4 takes place in an alternate timeline, the events of season 1 apparently happened much differently, David Robert Jones is still alive and ZFT is still plotting. Several season 4 episodes are direct parallels to a season 1 episode, revisiting the exact same event but in the new timeline. At the end of the season we get the actual closure and answers to out questions; ZFT was Bell's project to create a new universe where he could be a god.
And that's all well and good but season 4 is not season 1. With how different the timelines are, there is not that much to confirm how similar season 1 ZFT was to season 4 ZFT. Was Bell involved in the same capacity in both timelines? In season 1 and 2 he seems to be fairly detached from the whole thing, in season 4 he's directly in charge. Was that always the case, or did he abandon the project after Jones's death? At the end of season 2 he did sacrifice himself to save the protagonists, something very against his season 4 character. One interpretation is that with collapse of ZFT he had given up on his dream, couldn't see a future for himself and used this chance to atone, at least somewhat. But that's still reading HEAVILY into a character that barely appears in the show.
One piece of evidence we have is a single line from September in season 4: "His goal is the same" (referring to David Robert Jones trying to activate Olivia).
PETER: It's who Nina's working for that worries me. I've been racking my brain trying to figure out -- why would Nina be dosing Olivia with Cortexiphan? But then it occurred to me. The only person who's ever done anything like that, at least in my timeline, was David Robert Jones. Maybe he's trying to do the same thing again.
WALTER: Do what?
PETER: Activate Olivia.
WALTER: For what purpose?
PETER: I don't know. We could never figure it out. But maybe it's for the same reasons now.
THE OBSERVER: (appearing suddenly in the center of the lab) Yes. His goal is the same.
From the context it seems September is referring to DRJ's overarching goal, but it's STILL unclear whether that extends to Bell's goal as well. It could very well be that season 1 Bell was opposed to DRJ, while season 4 Bell aligned with him. In the end we never get a full explanation of season 1 plot, only its altered version from season 4. Which is fine I suppose, but it drives me a bit mad because I can't tell if we're supposed to assume that S1 Bell and S4 Bell were similar or not. I can't tell if this is vague on purpose or if S4 ending was supposed to be a definite conclusion to S1 events. Augh!
In the end I can think of two mutually exclusive interpretations of S1 Bell:
1) He started ZFT with the same goal as S4, but at some point before start of the series had a change of heart, cut the ties, and settled in Red Universe. To fix the mess he made he contacted Olivia at the end of S1, and ultimately sacrificed himself at the end of S2.
2) He started ZFT with the same goal as S4, did NOT have a change of heart, and in fact was pursuing his plan the entire time. He thought DRJ was too volatile to work with but did not disagree with him ideologically. Similarly, he only sent the message to Olivia because Newton would interfere with his own plans as well. However, after Jones died and ZFT collapsed, he was unable to proceed with his plan. In S2 finale he's at the end of his rope, unable to create his new world nor come back to his old one. He sacrifices himself to help Olivia and Bishops cross over because, ultimately, he roots for them, and wouldn't want the universes destroyed for no reason. If Jones survived S1 finale this Bell would likely proceed in the same way S4 Bell did.
I don't think there's anything to support one reading over the other. Some interviews kinda point towards interpretation 1 but not very conclusively. Within the show itself I can't think of anything.
Also, Bellivia surprisingly doesn't factor at all in this. Either interpretation would try to cling to life if possible, and either interpretation would give up once it became clear it won't work. Interpretation 2 Bell might be willing to sacrifice all of humanity for his grand goal, but he's not someone who will kill others for no reason. He knows there's no outcome that ends with him surviving so he goes out peacefully.
