[Warning: This story contains major spoilers from Friday's Fringe finale. Read at your own risk.]
Let's travel back in time, or rather forward, to find out how the grim future came to be:
After entering the machine, Peter lands 15 years in the future, where our universe is being torn apart. While Peter initially remembers he had time-traveled, by the time he's out of the special Fringe medical facility, he has fully integrated into this era.
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Peter — who's now a full-fledged agent and is married to Olivia, the head of the Fringe Division — is thrust into a mission after the End-of-Dayers set off a lightbomb in the opera house, a nice throw back to the end of last season, where Walter (John Noble) and Olivia (Anna Torv) had departed for the other universe.
The only person who can deconstruct one of the unexploded lightbombs — a device used on the soft spots to rip holes in the fabric of the universe — is, of course, Walter, who has been behind bars since the machine destroyed the other universe 15 years ago, setting off a chain of events that have created nearly unstoppable cracks in our universe that the Fringe Division try to keep at bay with amber.
As Walter and the Fringe Division try to crack the lightbomb, Walternate plans to open the wormhole in Central Park, which oddly connects to prehistoric times. This location is sentimental to him because it's the location of the wormhole that opened up in his universe, obliterating everything and leaving Walternate, who left for our universe to garner a peace offering, stranded.
As a last act of vengeance, Walternate lures Peter to a secluded cabin, where he takes pleasure in telling Peter that he will make him suffer as much as he did in losing his universe. It was a trick all along, though, as Peter realizes too late that Walternate is a mere hologram and the real Walternate is back at Central Park shooting Olivia point-blank in the head.
Walter has deduced that one universe can't survive without the other, so when they destroyed Walternate's universe, they sealed their fate. "That was the day we died," Walter says. He suggests that Peter go back into the machine, which will send him back to 2011 so they can prevent their past selves from making the same mistakes.
Walter has also realized how the machine pieces were buried millions of years ago by the First People: Walter, himself, sent them through the wormhole in Central Park, meaning they have made these mistakes at least once before, and are, once again, attempting to reverse their fate.
We flash-back to the present, where Peter, still in the machine, comes to. Joyful to see Olivia alive, he merges the two universes on Liberty Island, where the machines are held, to act as a gateway where they can work together to save both universes. As Peter tries to explain this, he suddenly and mysteriously disappears out of thin air! Immediately, Walternate goes on the offensive, once again bringing up the argument that Walter destroyed his universe, but Olivia says they must all now work together. (Notice Walternate's argument was about the destruction of the universe, not about the kidnapping of his son so many years ago that set everything in motion.)
Outside the building, a group of Observers have gathered to note that Peter has already been forgotten by the group. Why? He never existed! Once Peter fulfilled his duty to unite the two universes, he disappeared. Yeah, that's right, he disappeared! Peter was seemingly created as a means to an end: Either destroy the universes or bring them together.
Is your mind blown? Yeah, us too. What did you think of the season finale? Are you more confused now? Are you worried whether Joshua Jackson will be back next season? Do you feel cheated because Peter never really existed? Hit the comments with your thoughts.