Bell takes Walter into the cabin on his freighter and shows off his hologram projection program of the new universe that he plans. He promises that the real one will be even better, and that he has set the final pieces in motion and there's no way to stop it. Bell believes that Walter's presence there at his supreme moment is an act of providence.
Peter and Olivia arrive at the Harvard lab and find no signs of Walter or Astrid. They find the lemon cake Walter was baking and wonder if they went out to breakfast. As Olivia makes coffee, Peter ask if she wants to talk about how she can suddenly do things with her cortexiphan abilities that she's never been able to before. He wants Walter to run some tests on her when he gets back and Olivia agrees. Jessica calls her and says that she didn't know who else to call. She tells Olivia that someone has been following her since she left Harvard, and Olivia tells her to stay there and lock the doors. As Jessica hangs up, she's seemingly unaware that the Observer September is in the house with her. As he steps forward, a glowing rune appears at his feet, stopping him.
Peter and Olivia drive to Jessica's house in Quincy, MT and find her purse and cell phone on the table. A large chunk of the floor has been removed but they find nothing else. Peter assures Olivia that she didn't put Jessica in danger. Broyles calls to tell them that Astrid has been admitted to Boston General with a gunshot wound but is in stable condition. However, Walter isn't with her. They meet with Astrid at the hospital and she explains that she and Walter went to the waterfront warehouse to find Bell. Broyles tells her that she wasn't found at the warehouse and they figure someone moved her and called 911. Astrid apologizes to Peter for failing to get Walter out and he assures her that it's okay. She gives them the address and informs them that she heard animal noises that she didn't recognize, and Peter suggests that they go there even though it's likely they already moved on. As they leave, Astrid tells them to be careful.
As they arrive at the A1 Import warehouse, Olivia wonders how the nanites and the solar beam are connected. They go inside and find the Observer standing there, his feet fastened to the section of floor removed from the house. Jessica comes out with a gun and orders Olivia to drop her weapon. Olivia reluctantly does so and Jessica explains that the stasis runes have trapped September, and they're in a future that he didn't predict. Bell figured that if they put Peter in danger then September would come to investigate. Jessica shoots at him three times but he catches the bullets, and she explains that the Observers can operate at hyper-attenuated time. She then takes out a gun created by Bell that shoots faster and hits him in the chest. Olivia asks Jessica what she wants and the woman explains that September feels no emotion or pain, but it's clearly upsetting Jessica. Jessica fires again but Olivia gestures and sends the bullets back, killing her.
Olivia goes to September, who admits that he's surprised they know the methodology to create the stasis rune. Peter breaks it and September tells them that he doesn't know where Walter is. Olivia explains that she saw him at the opera house when he was wounded in his future, and he told her that she would have to die in every version of the future. September admits that he didn't, or wouldn't, but he understands that he will. He tells them that he hopes he'll get back to them in time and then vanishes.
Peter takes Jessica's corpse to the lab and hooks her up to Walter's mind-linking device. Nina arrives with the neural device that Peter knows about from his own timeline, and they inject bolts into Jessica's corpse. Nina then talks to Olivia and assures her that they'll soon know what Jessica knows. Olivia figures that Jessica risked her life to engender her feelings and figures that Bell is trying to activate her cortexiphan abilities. Nina points out that she's already had a vast potential for compassion and believes that Bell needs something from Olivia, something only she can provide.
Aboard the freighter, Walter asks Bell what he hopes to gain by destroying both universes. Bell says that Walter was the one who inspired him when he created a universe that operated under his rules to save Peter. When he got scared, Walter asked Bell to cut out a portion of his brain. But as Bell grew older, he grew cynical and gained cancer. He doses himself with cortexiphan to slow it down and then realized that Walter was right and it is their destiny to be gods. Walter denies it but Bell points out that he has always played God, and now he is too.
Peter finishes prepping Jessica's corpse and they tap into her fading neural network. They demand to know what she's done to Walter but she starts reverting mentally. Olivia tries to get through to her but Jessica starts talking about her bicycle bell. Nina tells her to focus but Jessica continues rambling on, saying that he has gone to sea. Peter realizes that Bell is on a boat near the warehouse, and Jessica tells them that Bell is the birth of a new world. With time running out, Olivia asks Jessica how Bell plans to collapse the two universes, and Jessica says that Bell needs a power source and they're all expendable. Olivia grabs her arm and there's a burst of energy. As Nina has Peter get her a gauss meter, Olivia realizes that she's the power source and Bell has activated her to engineer the collapse. However, Nina says that she has a way to find Bell if he's using that energy.
At Fringe Headquarters, Broyles' team confirms that Bell's freighter fell off of radar six hours ago. Nina brings Broyles up to speed and explains that they should be able to identify the dimensional frequency that Olivia is now vibrating at. That frequency will match the safe point where Bell will take refuge when the two universes collapse. They get a fix on navsat but also detect a series of microquakes and storms as the universes start merging.
Olivia goes into the conference room and Peter goes in after her. He tries to reassure her but Olivia doesn't believe it. She remembers the cortexiphan trials and how she was all alone with Bell experimenting on her, and says that nothing has changed. Peter assures her that this time she isn't alone and hugs her.
Bell calls Walter over to the window and shows him the vast storm that is forming around the freighter at the dimensional safe point.
At Fringe Headquarters, the technicians pinpoint the frequency and the team takes choppers out to the coordinates.
Walter begs Bell to stop, but Bell tells him that they deserve this.
There's nothing at the coordinates but only Peter can see the freighter. Nina realizes that the fabric between universes is growing thin. The ship has phased out of sync with their universe but Peter can see it because he resonates at a different frequency. Peter points out that there's no way to get to the other universe, but Olivia says that she can do it. Nina agrees, saying Olivia can jump between worlds. They will need to work together, and Nina assures Olivia that she had the power all along and couldn't access it because she was denied the knowledge.
Peter and Olivia step out on the chopper's landing strut and concentrate, and then jump. They land on the freighter in the other universe and Peter almost falls overboard until Olivia pulls him back. They go down below and realize that the freighter is Bell's ark.
While Bell recites poetry from Yates, Walter grabs a gun and loads it. However, Olivia and Peter arrive. Bell admits that he had hoped he and Walter would die off and that his new race would grow on its own. However, he welcomes them as his new Adam and Eve. When Peter demands that he shut it down, Bell says that Olivia is a living uncertainty machine and she's fueling the process. Walter turns, asks Peter to forgive him, and then shoots Olivia in the head. The storm fades and the freighter reappears in its own reality.
As Peter goes to Olivia's side, Bell congratulates Walter, who is aiming the gun at him. He rings a bell on a table and fades away, saying that they could have been happy together. Walter then goes to Peter and tells him that time is of the essence if they're going to save her. He has his son put Olivia on the desk and explains that if he can get the bullet out before the cortexiphan wears off, it will regenerate her damaged brain. Since there's no exit wound, he cuts into the back of her skull with a letter opener and uses an extendible map pointer to push the bullet out. After a moment, the wound heals and Olivia stirs.
Back in Washington, Broyles meets with Senator Van Horn. The senator informs Broyles that Bell's genetic specimens will be cryogenically quarantined, and his committee grants their request for additional funding as thanks for saving the world. Van Horn adds his personal congratulations and informs Broyles that he's been promoted to general. Outside, Broyles tells Nina that he'd like her to run their new science division and she chuckles.
Peter and Walter wait at the hospital, and Walter suggests that the cortexiphan levels in Olivia's body should be negligible now and she should be normal for the foreseeable future. Astrid joins them as the doctor informs them that Olivia is good to go. Peter goes to see her while Astrid sits with Walter and offers him some red licorice. He thanks her, getting her name right for the first time.
Peter shows Olivia the apartment that he's found for them, figuring that they deserve something normal. He points out that September was right and she had to die, but Peter refuses to lose her again. He embraces her, but Olivia pulls back and tells him that the doctor has confirmed that she's pregnant. As they kiss, Walter and Astrid come in and watch, smiling.
Later at the lab, Walter is making toast and looks up to see September standing there. The Observer says that they have to warn the others that "they" are coming.