On the other Earth at Fringe headquarters, the team detects a breach. Charlie, Olivia, and Lincoln Lee Lane arrive and Colonel Broyles tells them. As the team banters, they head to the breach site in New York and secure the theater in question. Lee detects degradation and informs Broyles, who orders a quarantine. Olivia interrogates the people outside while Lee checks for decreased gravity.
Back at Fringe Headquarters, Broyles calls in Agent Astrid, who confirms that quarantine will cause 10,000 casualties. As Lee prepares the quarantine device, Astrid concludes that the event is terminating and quarantine is unnecessary. Lee shuts down the quarantine device, and Charlie informs them that they've found a dead man, covered in carcinomas. They check the corpse for ID and discover strange dollar bills. They're unaware that Walter, Olivia, and two others are sneaking away.
36 Hours earlier
At the lab, Walter watches a surveillance tape showing his alternate talking to Peter and inviting him to come with him. Peter agrees and they teleport away. Walter gets an idea and starts digging through his boxes.
Olivia is at a bar, drinking. She looks up as the Observer leaves after placing a piece of paper next to her. Before she can investigate, Walter calls to tell her that there's something he needs to remember. Olivia discovers that the Observer has left a piece of paper with a picture of Peter with energy glowing from his eyes, and a man mounted in some vast machine.
Olivia meets Walter at his home and he explains that the paper she has is what he's supposed to remember: that Peter returning to the other universe will cause the destruction of their Earth. They get Broyles and take the information to Nina Sharp at Massive Dynamic, and tell her that she has to help them cross over.
In the lab, Brandon explains that the two universes overlap. When someone passes through, their cells separate, but they don't remerge with the same cohesion. Brandon doesn't know how Bell passes back and forth, but warns that he's become molecularly unstable. Nina admits that Bell hasn't communicated with her since he passed over. Walter warns that his process to open a door could shatter both words. Nina sends Brandon out and then explains that Olivia has the ability to cross over safely. Olivia insists she has no control, but Walter suggests that with more cortexiphan children, the psychic energy could prove sufficient to send them through. Unfortunately, Olivia is the only successful cortexiphan child left. However, Broyles notes that there are more.
Broyles takes Olivia to Massive Dynamic's experimental campus. He explains that they have found five children, and Massive Dynamic has three subjects that have mastered their abilities. Broyles takes her to see the three, including: James Heath, who can heal disease; Sally Clark, a pyrokinetic; and Nick Lane, who can empathically transfer emotions.
Olivia and Broyles take Nick, James, and Sally to a special lab at the Boston Federal Building, which Peter demanded funding for from the government. When they see Walter, he apologizes to them for what he did to them. However, he insists that he and Bell felt they needed the children as protectors to save both universes. After Walter leaves, Nick thinks Walter has changed but James doesn't believe it. Broyles tells them that Walter has found a spot for transition and tells them to get some rest, but James asks for a night off. Broyles agrees to his request.
James goes to a hospital and uses his ability to heal the patients.
Nick and Sally go to a hotel and have sex, using his empathic transfer abilities.
Walter goes home and goes through his clothing, and prays to God for Peter's safe return.
Olivia sits over Ella's bed until she wakes up. She then gives her niece a necklace that Olivia's mother gave to her, saying it would keep her safe. As Olivia leaves, Rachel asks when she'll be back and Olivia reassures her and gives her a hug. Once Olivia has left, Ella shows her mother the necklace and Rachel realizes that something is wrong.
When Olivia returns to the lab, she tells Broyles that Nina has sent a message for him to meet them at Grayshot Bridge in Central Park. Broyles warns that Bell may be working for the enemy to create the weaponry shown on the paper, but Olivia notes they don't have any choice.
Walter takes Olivia and Broyles to the theater where the others have gathered. He has the four cortexiphan children form a circle around him to bring him over. Broyles refuses to let Walter endanger himself, but Walter refuses to ask them to do something he won't risk himself. Broyles gives in and Nick tells Walter that perhaps he did something good by experimenting on them.
Walter has the four cortexiphan children go into a mild trance. They transition over and James immediately collapses. Sally doesn't feel well, and Walter insists they have to hide. They take refuge and Walter tells Nick to empathically force them to leave, but he's unable to use his abilities. They watch as the alternate Fringe team realize that James, dead of cancer, may be from an alternately reality. They report to Colonel Broyles, who informs them a scan of one of James' $20 bills raises a red flag at DOD.
The Fringe team is summoned by the Secretary, Walter Bishop, who asks for an update on their investigation. He then asks for Olivia to describe the Fringe Division, part of the Department of Defense assigned to investigate environmental disasters caused by dimensional breaches. The Secretary wrote about it in ZFT, but tells them that the holes led to another universe. They were created by someone deliberately, and that James is from the alternate universe and came with others. The Secretary tells them to find the invaders and the team leaves.
Olivia and the others take to the streets and try to take a bus, only to discover that they need ID. They have no choice but to walk to Central Park.
Peter wakes up in a bedroom, attached to medical monitors. He unhooks himself and explores the house, and finds the alternate world's version of his mother, Elizabeth. After a few awkward moments, they embrace, crying.
Sally gets increasingly worse as they walk, and Walter wonders if they overused their abilities the previous night. He suggests that Bell might be able to help her.
Elizabeth and Peter talk outside, and she explains that coffee is rationed. Peter mentions his mother on the other side, and then wonders if Elizabeth wants to hear about her. The alternate Elizabeth insists on hearing all about his childhood, and he explains that she committed suicide 10 years ago because she wasn't strong enough. She then explains that Walter is staying in the city, but asked her to give Peter a book of blueprints.
As they go past a toy store, an increasingly ill Sally notices the dolls and says that she wants to stay.
Peter goes over the blueprints.
Olivia and the others get to Central Park and Grayshot Bridge. The police move in and Walter believes that Bell has betrayed them. Walter and Olivia run into the woods, while Lee shoots Nick when he tries to help Sally. He approaches them and recognizes Nick, and then watches as Nick dies. Sally kisses Nick and then summons a fireball and incinerates herself, Lee, and Nick's corpse.
The alternate Olivia tries to track down Walter, firing a shot, but is called back. She can only stare at her partner, charred to the bone.
Walter and Olivia are separated. He walks the streets on his own, and realizes that the alternate Olivia managed to shoot him. Walter gets to a hospital and collapses.
The alternate Elizabeth talks to Peter, who admits he's not sure what they mean.
Olivia evades the police and uses an information kiosk to look up an address.
The alternate Olivia returns home and tells her boyfriend Frank Stanton that Lee will recover after several weeks of nanite regeneration. She lies about her work and he offers a back rub. Outside, Olivia watches from the street as they embrace. Bell comes up behind her and explains that he figured she would go to her alternate's apartment. By the time he arrived at the park, it was too late. Bell warns her that she'll have to trust him, and that they don't have much time to rescue Walter.
The Secretary goes to a secret facility where the weapon is being assembled. He takes a power sink out of a case and leaves.