In the past, Elizabeth Bishop is cleaning her home when she realizes that peter has let a note saying that he's going home. She runs out to the lake, where Peter from the other world has tied a concrete block to himself. He smashes through the ice and falls in, and Elizabeth dives in after him. She manages to untie him and get him back to the house, while he screams at her that she's not his mother.
At Jacksonville, Walter is putting the cortexiphan children through exercise. A young Olivia is talking to one of the boys, and Walter tries to get her to focus. His aide, Mrs. Ashley, comes in and says that Elizabeth has called. Walter dismisses the class early and goes home, where he tries to convince Peter that he's in his world. Peter doesn't believe it and insists that he wants to go home. Once they're alone, Elizabeth warns that they can't keep up the deception, but Walter insists they have no alternative. He can't create another portal because the gap between universes has been weakened by his first attempt. Elizabeth says that she can't deal with Peter if he can't trust her, but Walter says that he plans to use the cortexiphan children to cross over and take Peter with them. He asks Elizabeth for a little more time and she reluctantly agrees.
At home, Olivia's stepfather tells her to go to bed. She runs away from him and finds herself suddenly standing in a field with something looming over her. After a moment, she finds herself back at home.
The next day, Elizabeth makes breakfast for Peter, who insists that he can tell she's not his mother and that Walter stole him from the world at the bottom of the lake. He insists that he's not crazy, and Walter has abducted him.
Walter returns to his office and tells his aide that he wants to separate the children and begin independent training. He notices that Olivia is on her own, and Ashley says that the girl didn't have a good night. Walter goes to see her and notices that she has a black eye. Olivia insists that she tripped, even when Walter clearly doesn't believe her. He notices her drawing an airship and recognizes it from what he's seen of the Other Side. Walter confirms that she saw it the other night when she fell.
Elizabeth takes Peter for a drive and shows him a field of tulips that a scientist transplanted there. She asks him what he would do if he could change the world, and Peter says that he'd go home. Elizabeth tells him that she has a surprise for him, and takes him to a toy store. She asks him to stay there and pick a toy, and then watches as he looks around the store. Peter picks up a toy airplane and smiles.
Walter tells Miss Ashley to prepare some experiments to test Olivia, and theorizes that emotional stimulus triggered her ability to cross over. Elizabeth arrives with Peter, who notices Olivia. While they exchange glances, Walter tells Elizabeth that Olivia may be the key to getting Peter back.
As he prepares to videotape Olivia's tests, identifying her as Subject 13, Walter writes a note to William Bell, saying that he needs some help and wants him to review the footage. He tests her emotional responses and gets no response. Walter notices her watching Peter, and then concludes that fear might work best. He turns off the lights in her lab and scares her with Nick, a boy posing as a corpse, and she transitions.
At the Bishop home, Peter plays with his plane, while Elizabeth hears fire trucks going by. She tries to call and discovers the phone is dead, and tells Peter to come with her.
Walter sends Nick on his way, and then tries to figure out what he's missing that relates to Olivia's ability to translate. Ashley warns him that there's a small problem, and then goes outside to greet Elizabeth, who figured something had happened at the lab. She asks what happened and Ashley explains that one of the cortexiphan children has gone missing. Elizabeth has Peter wait in the common area, and he notices Olivia's cubby. He takes out her sketch pad and looks at it, and sees one picture that she's drawn of her father as an ogre. Another picture shows the field of tulips he saw earlier.
Walter arrives in his office and finds Elizabeth going through Olivia's file. She's discovered that Walter has recommended that they return Olivia to her home and her abusive father, because he believes that the combination of love and fear trigger her ability. He warns that if he doesn't, it could take him years to find a way to cross over. Walter admits that he stole Peter, and if they don't return Peter, the people on the Other Side will come after Peter, just as Walter would do in their position. Ashley comes in and explains that Peter isn't in the common area. Elizabeth goes out and finds the discarded toy airplane.
On the Other Side, Walter sits at home and drinks. Elizabeth tries to stop him, but he says that he doesn't have any other options. Later, Elizabeth makes dinner and Walter interrogates her about the man who took Peter. She dismisses his theory, insisting that there's no explanation. Walter insists that nothing is inexplicable, and they have to go over it until he comes up with a scientific explanation. However, Elizabeth insists that they don't have a marriage anymore.
Walter goes into Peter's room and contemplates the empty bed. He then goes to Elizabeth, who says that she prays every day that their son is safe and someone is taking care of him. However, she warns that their marriage is breaking and she can't bear to lose Walter as well. Elizabeth asks him to stay so they can put their marriage together.
The next day, Elizabeth wakes up in bed and discovers that Walter is gone.
Walter drives to Bishop Dynamic and enters his office. After taking a drink, he looks out at the shuttle launch pad nearby.
Ashley gives Walter Olivia's sketchpad, and the picture of her father as an ogre.
Peter finds Olivia in the field of tulips and explains that he knew she'd come there because it was the only drawing that looked happy. She warns him not to approach, but Peter says that he's not afraid and sits down next to her. Olivia explains that her stepdad gave her the black eye, and that Walter will send her home because she messed up. She doesn't believe that Walter will do anything about her abusive stepdad, and Peter talks about how his mother told him about how to change things. Olivia asks him if he trusts Walter, and Peter tells her to tell Walter.
At Jacksonville, Elizabeth and Ashley are talking to the police when Peter and Olivia come back. When she hears that her stepfather is coming to get her, Olivia insists on seeing Walter. She runs into her office and tells Walter that when her stepfather beat her, she crossed over into the other universe. Olivia begs him to stop her father. Walter comes in behind her, and Olivia realizes that the Walter she was talking to was in the other universe.
Walter takes Olivia to her stepfather, and he tells her that it's time to go home. However, Walter tells him that Olivia is special to him, and if anything happens to make her frightened or uncomfortable, he'll call Social Services and use his connections to make sure that the stepfather is put away. The stepfather backs down, and Walter tells Olivia that the next day they'll find a new way to activate her powers.
At home, Peter apologizes to Elizabeth for running off. He asks her if he's ever going back, and she tells him that sometimes the world they have is the world they want, and all they can do is use their hearts and imaginations to make the best of it. Elizabeth promises to take care of him no matter what. When Peter points out that she's not his real mother, Elizabeth claims that his illness has confused him and she's really his mother. Peter smiles and goes to wash his hands for dinner, calling her "Mom." Once he leaves, Elizabeth breaks into tears and then pours herself a drink.
On the Other Side, Walter calls to tell Elizabeth that he knows where Peter was taken.