"Fringe" started out as a show about weird science experiments carried out on the unsuspecting public, something that the "Fringe" division of the FBI referred to as "The Pattern." They were also in some way connected to experiments or ideas from the past of Walter Bishop, a once brilliant but now insane scientist who co-founded the immensely profitable and powerful Massive Dynamics.
"Fringe" wasn't massively popular however, which may be why it seemed to become a new show every season. At the end of the first season, the apparent baddie was killed while trying to enter a parallel dimension, very similar to ours, but where events happened slightly differently. For one thing, it soon became clear, Walter's son, Peter Bishop, died as a child in our reality, but Walter saved the Peter from the parallel world, brought him here and raised him as his own.
In addition, the main baddie was attempting to crossover to the other dimension because of William Bell, the missing co-founder of Massive Dynamics, who apparently moved to the other dimension years ago for some reason. Thereafter, the parallel dimension was the raison d'etre of the show. Walter's crossing over had apparently disturbed the balance of the two universes. The other universe was already dying, but ours would follow if something wasn't done about it.
Then it was determined that there was a machine, made millions of years ago by "The First Men," that could destroy one universe or the other. Walter's evil twin from the other universe, referred to as "Walternate," had the machine and wanted to use it to destroy our universe, but Peter was the key to activating it. Peter instead created a corridor in which both universes could come together and find a solution to the problem, but in the process he ceased to exist in either universe.
It wasn't certain the show would be picked up for another season, and if not, that would have been an intriguing way to end it. But it was renewed, and the show explored the consequences of Peter no longer existing, including that the death of the baddie from season one was undone. (It's a well-known time travel scenario that the changing of one event has ripples that affect everything else, as in Ray Bradbury's story "A Sound of Thunder" or the film The Butterfly Effect.)
However the new season also involved Peter struggling somehow to be reborn, and resulted in the true baddie being revealed as William Bell, who wanted to create a new universe from the destruction of the other two universes, one made in his image or according to his plan.
Was this the plot all along, or is this just the plot of the revised reality caused by Peter's temporary disappearance?
Now in its final season, Earth has been taken over by The Observers, bald men from a future earth that has become uninhabitable, who have time-traveled to take over our time. This will change the past, so their future will never come to be, but that's in part because they will use up our world before then. There is no apparent risk that this will cause them to cease to exist, as Peter's continued existence demonstrates.
I thought the changing scenarios from season to season were confusing and maddening, less like a well-orchestrated master plan than an arbitrary series of reboots by writers who didn't know where they were going and how to get there.
Now I think I was wrong: The Observers' plot was the true plot all along.
From season one, allegedly from episode one, an Observer has been seen in every episode, even if only in a crowd shot. Apparently the Observers have been working to create a reality where they can conquer Earth and survive. All of their machinations have been to thwart the villains -- the Pattern, the alternate universe, William Bell -- so they can step in and take over.
If so, it all makes sense now, but it's only sense that a science fiction buff is equipped to understand without some explicit explanation. I hope they take an episode to state this explicitly and show all the steps along the way that led to this future and make sense of it for everyone.