In William Bell's office on his ship of mutants, he shows Walter a holograph of his new world. The final piece is in motion. He couldn't stop if he wanted to - and he doesn't. Saying it's providence that Walter's there to witness this, Bell laughs madly.
Olivia and Peter find the lab deserted, and no answer on Astrid's cell. Peter, whose right arm is in a sling thanks to David Robert Jones, asks Olivia about the Jedi mind trick she pulled on the roof. It had to be the Cortexiphan.
Jessica Holt, the nanite victim Olivia saved, calls Olivia and says she's been followed ever since leaving Harvard. September the Observer walks toward Jessica, and a light glows beneath his feet. He stops, stuck. Olivia and Peter find Jessica's house empty, and a hexagonal hole in the floor.
Broyles phones Olivia: Astrid's in Boston General with a gunshot wound, but stable. They realize that Walter's missing. Astrid explains about the armed men at the waterfront warehouse, tearfully telling Peter she tried but couldn't get Walter out.
Peter and Olivia find the warehouse . . . where Jessica holds them at gunpoint. She works for Bell! September is trapped on that piece of her floor, due to the stasis runes drawn on it. In Bell's latest move to activate Olivia's abilities, Jessica fires three bullets, which September catches in midair. It's not magic, but tech that lets Observers move very fast. However, a weapon Bell invented does penetrate September's chest. When Jessica fires again, Olivia catches the bullets and flings them toward Jessica, killing her.
Peter scratches at the runes, freeing September. Olivia says now they know how he got shot, recalling the opera house, where September said that in every version of the future, Olivia had to die. This hasn't happened yet for September, who disappears to investigate further.
Nina Sharp provides Massive Dynamic tech so Olivia and Peter can posthumously question Jessica at Harvard. They learn about Bell's own Noah's Ark. Nina says that Olivia's capacity for feeling, her incredible compassion, made William and Walter want her for the trials. Now, Bell needs something from her - which Jessica reveals is the energy to collapse the universes. That's why he activated Olivia, who's giving off some extraordinary electromagnetic energy.
Walter asks why Bell would do this, and he says it was Walter's idea. Peter died, twice. Walter hated God. He decided to create a universe that would operate by his rules. And then, frightened that he was smart enough to do it, he had Bell remove part of his brain. After Bell got cancer, he realized Walter was right. God made us in his image. If we are capable of being gods, it is our destiny.
At Fringe HQ, agents identify Bell's freighter, the Talos. Nina tells Broyles they'll find Bell where the universes are overlapping by pinpointing the area that matches Olivia's frequency. The collapse begins.
Privately, Olivia tells Peter she remembers how scared and alone she was during the trials. Nothing's changed. She's still that little girl, being used. Peter says something HAS changed. Now, she's not alone.
Walter eyes a vintage handgun in a glass case. Above the Talos, a huge vortex swirls in the sky.
Nina, Olivia, and Peter hover in a helicopter above the freighter, which is already out of sync with this universe. It's still visible from the Other Side, so only Peter, who's from there, can see it. And since Olivia now has as much activated Cortexiphan in her system as the original-timeline Olivia, she can cross over. She's had the power all along, just like in "The Wizard of Oz."
Bell recites William Butler Yeats' "Lake Isle of Innisfree" as Walter loads the gun. Peter and Olivia burst in. Bell says Olivia is a living uncertainty engine. Every breath she takes, every beat of her heart, tears the world from its hinges.
Walter shoots Olivia in the head!
Peter screams NOOO! The vortex disappears, and the collapse stops. Bell says very clever, old friend. If that's what you consider learning a lesson from the past, you paid a steep price. He rings a bell and vanishes.
Walter pushes his sobbing son off Olivia, saying Peter knows very well that death hasn't always stopped him. He SLAPS Peter to attention. Olivia's brain is saturated with Cortexiphan, which has temporary regenerative properties. It will repair itself - if Walter can get the bullet out in time. It's gruesome, but he does. They wait. It works! As Olivia heals, father and son weep with relief.
At the Capitol, Broyles is informed that Bell's missing, but his creations have been cryogenically quarantined for future study. The committee is funding upgrades to his operational and scientific divisions. Also, he's General Broyles now.
Outside, Broyles tells Nina that he has a fully funded science division . . . and no one to run it. Want a job?
At Boston General, Walter tells Peter that Olivia has in effect reversed what he and Bell did to her. The abilities could possibly reemerge someday, but basically, she's normal. As Peter goes to her, Astrid offers Walter some Red Vines . . . and Walter calls her by her real name.
Peter shows Olivia a house ad, saying they deserve a bit of normal. Good, because Olivia's pregnant! They kiss as Walter and Astrid look on. Everyone's together, and happy.
Later, Walter's making peanut butter and jelly toast while whistling "Rock-a-Bye Baby." September appears and says, "We have to warn the others: They are coming." Who?