Aboard the freighter Talos
, Bell shows Walter a virtual representation of the new universe that he plans to create. He assures Walter that the new one will be even better and that there’s no way he can stop the collapse of the two universe. Bell speaks of God and how he believes that Walter’s presence at the moment of his triumph is a sign of divine providence.
peter and Olivia arrive at the lab and discover that Walter and Astrid are gone, and wonder if they went to breakfast. As Olivia makes coffee for the two of them, Peter asks if she wants to talk about the sudden manifestation of her cortexiphan abilities. She agrees to have Walter run some tests on her when he gets back. They’re interrupted when Jessica Holt calls and tells Olivia that someone has been following her ever since she was at the lab after the nanite infestation. Olivia tells her to stay in her house and lock the doors. Once Jessica hangs up, September appears behind her, but discovers that he’s unable to move as a glowing rune appear beneath his feet.
When Olivia and Peter arrive at Jessica’s house, they find no sign of her. Peter discovers that a large chunk of the floor is missing, unaware that it’s where the Observer stood when Jessica called. Olivia worries that she somehow put Jessica’s life in danger, but Peter assures her that she had nothing to do with whatever happened. They’re interrupted when they receive a call from Broyles informing them that someone placed an anonymous 911 call about Astrid, who was shot. They go to the hospital and confirm that she’s in stable condition, but are surprised to discover that Walter isn’t with her. She tells them that she and Walter went to the waterfront to find Bell, and Broyles tells her that she was moved. Astrid apologizes to Peter for failing to escape with Walter, and he assures her that it’s okay. Once they have the address of the warehouse from Astrid, Peter and Olivia leave to see if they left any clues behind.
As they arrive at the Olivia, Olivia wonders what Jones’ master plan is since it involves nanites and solar beams. Inside they find September in the middle of the warehouse, standing on top of the piece of flooring from Jessica’s house. He’s still unable to move due to the rune. Jessica emerges from the shadows and holds a gun on Olivia, telling her to drop her weapon. Olivia has no choice but to do so and Jessica explains that they’re in a future that the Observers didn’t protect, one where she traps him with a stasis rune. She works for Bell, who concluded that if they endangered Peter then September would come to observe. Jessica then fires three bullets at September, who easily gets them. She explains to Olivia and Peter that the Observers use technology to reach a hyper-attenuated temporal state. However, she has a gun that Bell created that fires even faster. She shoots at September and hits him in the chest. A frantic Olivia asks what she wants and Jessica points out that the Observer feels no pain, but clearly Olivia is upset at his plight. She prepares to shoot him again, but Olivia concentrates and flings the bullet back into Jessica, killing her.
Olivia checks on September, who dispassionately admits that he didn’t expect Bell to be able to create a stasis rune. Once Peter breaks the rune, the Observer can move and tells them that he doesn’t know Walter’s location. Olivia tells him about how she saw him in the opera house on the Other Side, bleeding from the same wound, and that he told her that she had to die in every reality. Surprised, the Observer says that he will say that to her but hasn’t yet, and goes back in time to see why he said it.
With time running out, Peter takes Jessica’s corpse to the lab and starts hooking her up to Walter’s cerebral scanning device. Nina arrives with the neural device that Peter knows about from his timeline, and they prep Jessica for temporary revivification. While they wait, Nina tries to reassure Olivia, who now believes that the whole plan was designed to trigger her feelings and activate her cortexiphan abilities. Nina suggests that Olivia has something Bell needs to merge the universes and destroy them.
Aboard the freighter, Walter tries to get through to Bell, who explains that he got his idea from Walter. Walter was the one who first sought to create a universe where Peter was still alive. When he panicked at the idea of such power, Walter asked Bell to cut out the pieces of his brain containing the knowledge Later, Bell discovered that he had cancer and dosed himself with cortexiphan to inhibit its spread throughout his body. However, it was only a temporary measure and he realized that he needed to play God, just as Walter had.
Peter finishes attaching the device to Jessica’s corpse and they activate her fading neural pathways. Shocked that she is dead but still conscious, Jessica rambles on when they try to question her. All they can determine is that Bell is on a boat somewhere near the warehouse, and that he plans to create a new world. Olivia manages to get through to her and Jessica says that Bell needs a power source. Frustrated, Olivia grabs her arm and there’s a burst of energy. Jessica dies for good and Nina scans Olivia to confirm that she is now emitting vast amounts of energy. They realize that Bell is using Olivia’s energy to create the collapse but assures them that they can track the energy.
The team goes to Fringe Headquarters and the techs determine that Bell’s freighter disappeared off of radar six hours ago. Nina tells them to identify the dimensional frequency that Olivia is now vibrating at and look for the same frequency, which will be the safe spot that Bell has chosen to ride out the destruction of the universes. As they start to get a fix, a series of microquakes strike the world and they realize that the universes are starting to collapse. While they wait, Olivia goes to a conference room with Peter, who tries to reassure her. She points out that when Bell experimented on her in Jacksonville, she was alone and helpless and nothing has changed since. Peter tells her that this time she isn’t alone and they embrace.
Bell calls Walter to the window and shows him that they are within the dimensional safe spot, at the eye of a vast storm. As they talk, Walter notices an antique gun in a case.
The technicians pinpoint the dimensional frequency of the freighter’s location and Broyles has the team depart in choppers, heading for the location.
Walter tries to stop Bell but the scientist says that they both deserve what is coming
When the choppers arrive at the coordinates, there’s no apparent sign of the freighter. However, Peter tells the others that he can see it and Nina realizes that the ship has slipped to the Other Side. Since Peter resonates on a different dimensional frequency, he can see it while the others cannot. Peter has no way to cross over, but Olivia says that she can do it and Nina agrees. She explains that the two of them will need to work together, with Peter guiding Olivia as she makes the transitions. When Olivia worries that she can’t do it, Nina assures her that she had the power all along and couldn’t access it because they denied her the knowledge to realize what she could do. Peter and Olivia step out onto the landing struts, prepare themselves, and then jump where Peter directs them. Olivia transitions them and they land on the freighter on the Other Side. As they look for Walter and Bell, they find Bell’s collection of genetic mutations and realize that the freighter is his ark for the new universe
While Bell recites Yates, Walter takes the gun from its case and loads it. Before he can do anything, Peter and Olivia burst in and hold Bell at gunpoint. Bell admits that he didn’t want any humans in his new world, and that he believed he and Walter would die out, leaving his new race to develop free of mankind. However, he tells Peter and Olivia that they will be the Adam and Eve of his new universe. Peter tells Bell to shut down the process but the scientist boasts that Olivia is powering the process and it can’t be shut off. Walter raises the gun, asks Peter to forgive him, and then shoots Olivia dead center in the forehead. The storm instantly disappears and the freighter return to This Side.
A surprised Bell congratulates Walter on his decision, but then goes to a bell on a nearby table, rings it, and disappears. Walter goes to Peter, who is cradling Olivia’s body, and tell his son that they don’t have much time. They put Olivia on the deck and Walter explains that the high levels of cortexiphan will allow Olivia’s body to heal the damage... if they can get the bullet out. Working quickly with a letter opener and an extendible map probe, Walter cuts a hole in the back of Olivia’s skull and then uses the probe to push the bullet out. As Peter and Walter look on, the wound heals and Olivia stirs.
later, Broyles meets with Senator Daniel Van Horn in Washington. The senator assures him that all of Bell’s genetic mutations will be kept in storage, and passes on the committee’s congratulations on their saving the world. Van Horn assures Broyles that they’ll get all of the funding they need and offers his personal congratulations. He addresses a surprised Broyles as general, not colonel, and tells him that he’s been promoted. Once the meeting is over, Broyles leaves and meets Nina outside. When she wonders what happens, Broyles tells her that he has an opening in the new Fringe science division and would like her to fill it.
Peter and Walter wait outside Olivia’s room, and Walter tells his son that the energy expenditure should have used up all of the cortexiphan in Olivia’s body. There may be trace amounts that could have a future effect, but Walter dismisses them as inconsequential. Astrid comes over to join them as the doctor arrives and tells them that Olivia has a clean bill of health. While Peter goes to Olivia, Astrid offers Walter some red licorice and he gets her name right for the first time.
Peter shows Olivia the apartment that he has picked out for them and says that they deserve nothing. He assures her that he won’t lose her again and hugs her. Olivia hesitates and then tells Peter that the doctor has confirmed that she’s pregnant with their child. As they kiss, Walter and Astrid come in and watch quietly, smiling.
Sometime later, Walter is in the lab making sandwiches when September appears behind him. He tells Walter that they have to warn the others that “they” are coming.