In the show Fringe, how many different timelines and universes are involved in the storyline of the series?
There have only been two universes throughout Fringe, and four timelines; minor S3/S4 spoilers ahead:
The primary story line takes place in the "prime" universe, which is effectively our universe at around the time the episode aired.
There is a single primary "parallel" world, called the "alternate universe". This universe becomes relevant mostly starting with the season two finale, and significant parts of seasons 3 and 4 take place there. The history of that universe is slightly different from ours. Walter uses the popular multiverse theory to explain it's existence, which implies that at some point in the past the two universes were one, though it's never clearly established when they deviated.
It was sealed off permanently at the end of season 4, and the producers have confirmed that we won't be seeing any of it in season 5.
There are other universes we see very briefly in one episode, as Walter tries to find another universe where Peter's disease was cured, but we never visit or hear about them again.
There have been several different timelines; the implication is that we have seen four (one mostly through exposition). One crucial difference among the timelines is what happens to Peter and Olivia and their child, as described by September. So far, we have seen or heard about:
- The original timeline, where Peter died in our universe and was saved in the Prime one. This one was never seen on-screen, only described or referenced by various Observers over the course of Seasons 3 and 4.
This is the one that happened off-screen, presumably in September's original past, what he wanted to go back and observe. Here, Peter presumably grew up in his own world and had a son with Fauxlivia that did something important in the future.
- The revised timeline, where Walter brought Peter over to the main universe and he survived.
This is the timeline that September created by distracting Walternate, causing Walter to cross over; the other Observers then spent the next few decades trying to "undo" that screw-up. In this timeline, Peter and Fauxlivia had a son that grew up and did something horrible in the future.
- The rebooted timeline, where Walter brought Peter over but he died at the lake.
This is the timeline that the Machine put in place at the end of Season 3, though what this means for the no-longer-existing child of Peter and Olivia is unclear.
- The current timeline; this is basically the rebooted timeline, except that Peter has been returned.
Peter and Olivia remember events as they happened in the "revised" timeline of Seasons 1-3, while the rest of both universes remember the events as they happened in the "rebooted" timeline of early Season 4.
September tells Peter that his team are able to operate "outside of time" and that there are a multitude of possible timelines, though unlike the parallel worlds, there does appear to be only one at a time, and there is one that the Observers consider "correct" and are trying to maintain.
There are 2 universes, this has been consistent throughout the entire series (so far). There are three universes, but one of them was only seen for a couple of scenes in 1x19, The Road Not Taken. Olivia witnesses the activation of the spontaneous-combustion twins in another universe, but not the one commonly referred to as "Over There" - in this one, the twins got activated at the same time, meaning they were indeed also treated with Cortexiphan. This universe was never revisited.
As for timelines:
- Seasons 1-3 are one timeline.
- In 3x22, The Day We Died, we get a glimpse at a second timeline - this is actually the "original" timeline, and shows how the machine got buried in the past of the Seasons 1-3 timeline.
- Season 4 (and so far in 5), is a third timeline.
- The Observers come from the future of a timeline that, seemingly, no longer exists. In 4x14, The End Of All Things, September mentions what should have happened (from their perspective of the past), and how he accidentally made it deviate. He also mentions at that time that the Observers have technology that allows them to exist outside of time, and that from our perspective, they are only one possible future.
So, 3 universes (so far, and one was only seen for a few moments in Season 1) and 3, maybe 4, timelines (so far).