In 1985, Walter addresses the military at their research headquarters in New York City. He shows them an advanced cell phone and informs them that they developed it by peering into another, parallel reality with technology ahead of their own. When they wonder how Walter obtained it, he explains that he peered into the other reality and duplicated the design. He takes them to the roof and he and his colleague, Dr. Carla Warren, show them a window-like device that lets them see into the other reality, where dirigibles dock at the Empire State Building.
In the modern day, Walter comes to see Olivia when she refuses to take his calls. He brings the window device with him and she reluctantly invites him in. He admits that he knew there would be a cost for bringing Peter over from the other reality, but Olivia warns they don't yet know how high a cost it will be. Walter demonstrated the window device and explains that Peter was dying from a savage genetic illness that was slowly and painfully killing him. When Walter couldn't find a cure, he created the window device to find a reality where there was another Walter with another dying son, and obtain the cure from him.
Walter watches his "Walternate" through the window and concludes he's mixing random compounds. The other Walter is unsuccessful and Elizabeth, Walter's wife, calls to summon him home. Walter agrees and when he arrives, Elizabeth explains that Peter is getting worse and wants to talk to his father. He assures her that he won't go up and goes to talk to Peter, who practicing finger-rolling with his lucky silver dollar. Peter gives the coin to Walter and says that he's not scared of dying. Walter promises that nothing will happen to him, but Peter dies in his arms.
After Peter's funeral, Nina Sharp comes over to offer her condolences. She explains that William Bell couldn't be there because of an important meeting at home. The Bishops go home and Elizabeth blames both of them for keeping Peter confined due to his illness so that no one would ever meet him and know how special he was. Walter insists that Peter had a good life, but wonders if Peter knew how much they loved him.
That night, Walter sets up the window device in Peter's room and brings Elizabeth to view it and see the other Peter, in his bedroom in the other reality. He explains what she's seeing and says that he wanted to show her that somewhere, Peter was alive and having a happy life. Walter tells her that now she can move on.
As Walter watches his counterpart, he realizes that he's not using a random process. A bald man enters the alternate laboratory, distracting the alternate Walter. The alternate is unaware that his cure has succeeded, but it destabilizes before he can turn and see that he's been successful. Frustrated, Walter smashes the window device.
In the alternate reality, the bald man, the Observer known as September, meets with two of his fellow Observers, December and August. He tells them that the alternate Walter discovered him in the laboratory when he came there to witness Walter develop the cure. he has altered the sequence of events, and the other two Observers tell him that he needs to restore the proper balance. When September wonders how, they say that the opportunity will present itself.
Walter is working on the cure at the lab when Carla comes in and realizes that he plans to travel to the alternate reality. He explains that his counterpart also has a lakehouse at Reiden Lake. Carla points out that their theories suggest opening a portal will destabilize both worlds, but Walter dismisses her concerns because of her religious beliefs. He tells her that he won't let Peter die and then fires her. She goes to warn Nina, who was unaware that Walter had already built a portal. Nina calls William Bell.
Walter takes his equipment to Reiden Lake and sets it up on the icy lake. Nina and Carla arrive to stop him, insisting that Bell would also want him to stop. Walter notes that Bell isn't there and has refused to take Nina's calls warning him of the supposed danger. He explains that Bell is the one who wanted him to open the portal, as a means to increase his personal wealth and power. He proceeds through the portal and Nina tries to stop him. He gets through and Nina's leading hand begins to destabilize because of the dimensional interface.
Walter makes it through safely but discovers that the vial with the cure has shattered. He goes to the lake house, where Elizabeth is trying to comfort Peter. He gives her the lucky silver dollar and she promises that he'll be fine. Once she leaves, Walter comes in and impersonates his counterpart. he tells Peter that he can cure him but needs to take him to Cambridge. As they leave, Elizabeth asks what is going on. Walter privately tells her that she stay there because Peter will need her to rely on once he's cured. Elizabeth reluctantly agrees and she gives Peter his lucky coin back. As they go, Elizabeth makes Walter promise that he'll bring Peter back, and Walter does so.
At the lake, Peter begins to question whether Walter is his father. Walter uses a remote to activate the portal from the other side and they pass through. They make it safely, but the ice shatters due to the energy exchange. Peter and Walter plummet into the waters and start sinking. They are rescued by September, and Walter wakes up in the Observer's car. The Observer tells him that Nina and Carla left to get medical attention, and that Peter won't last very long unless Walter "fixes" him. He pulls the car over and leaves so that Walter can drive to the laboratory. When Walter asks why he helped, September merely says that Peter must live because of his importance.
At the lab, Carla comes to help and Walter thanks her. Peter has received the cure and is recovering, and Walter says he'll take the boy back once his condition is stabilized. Carla leaves and Elizabeth arrives. She's shocked to see her "son," alive and well, and Walter explains that he brought him from the other reality. Elizabeth embraces Peter and starts crying, as Walter insists that they must take him back now that he's been cured. However, Elizabeth just looks at him as she hugs her son.
Walter admits that he couldn't take Peter back. He opened the first of what would be many cracks in the fabric of space/time... and his choice made it all possible.