On Liberty Island, Olivia is confined in a room and Dr. Anderson tells her that she's trying to help Olivia get her life back. Olivia insists that it isn't her home, but Anderson tells her that due to stress and a head injury, she's created a fantasy of being from an alternate world. Olivia doesn't believe it and explains that she works in Fringe Division. Anderson then shows her a photo of Olivia with her mother, but Olivia insists that it isn't really her mother. Next, Anderson shows her photos of Lincoln Lee and Charlie Francis, and asks if they are her partners. Olivia denies it, and Anderson then shows her a photo of Bolivia posing in an Olympic marksmanship event. Olivia insists that it's not her.
Anderson points out that the idea of alternate realities is ridiculous, and Olivia agrees that she thought it sounded insane when she first heart it. Next, Anderson asks her about Peter, and Olivia explains that he's a civilian consultant. When Anderson asks where the others are, Olivia admits that she doesn't know, but figures they went home without her. Olivia insists that what she says is true.
Walternate is watching the interview on a security camera, and he informs Agent Brandon that their process of transferring memories doesn't work. He tells Brandon to give her another dose despite the possibility it will kill her, When Brandon expresses doubt, Walternate says that they are at war with creatures that have damaged the fabric of reality and put them all at risk. He wants to get Olivia to help them understand her skill to move between universes, so they can win the war.
A soldier enters Olivia cell and takes her for a treatment. As he enters the security code for the elevator, Olivia memorizes it. She is then taken to a room and given injections despite her pleas for them to stop. As they give her a second injection, she has a seizure and they unstrap her. Olivia quickly subdues them, leaves the chamber, and takes out the solider. After grabbing his gun, Olivia goes to the elevator and enters the code, and leaves. She runs through the woods and comes to the edge of a cliff looking out over New York City. With the soldiers moving in, Olivia has no choice but to jump.
Olivia makes her way into Manhatan and forces a taxi driver, Henry, to take her where she wants to go using her stolen gun.
Colonel Broyles reports to Walternate that it's unlikely that Olivia made it across to New York City against the currents, but believes that if anyone could do it, she could. Walternate tells him to find her.
Henry wonders why Olivia is in a hospital robe, and she informs him that she's been held by the government and they've performed experiments on her. She notices a photo of his family, and Henry says that he doesn't need any kind of trouble. Olivia then has him park and get out, taking his ID. She then tells him to go into the nearby store and buy clothes, and warns him that she now knows where his family lives.
At the Department of Defense hospital, Lincoln Lee is undergoing physical therapy when Charlie Francis comes in. The two partners joke with each other and then Charlie tells Lincoln that their Olivia has had a complete psychotic break, and the alternate Olivia escaped with the others. Broyles comes in and tells them that Olivia escaped from the facility on Liberty Island.
Henry gets Olivia her clothing and starts driving, and comments that she has a tattoo of a sun on her neck. Olivia realizes that the authorities gave it to her to make her similar to Bolivia. When Henry notes that she sounds insane, Olivia insists that what she's saying is true. He drops the matter and Olivia tells him to take her home.
Broyles tells Lincoln and Charlie that they don't know where Olivia is going. Lincoln insists on dressing and searching for the next six hours until he has to go back to the hyperbaric chamber.
Olivia arrives in Brooklyn at the opera house where she arrived. She says he should stay for 15 minutes, and warns him that if he leaves before then, she'll go to his address. Olivia approaches the opera house and a policeman assumes that she's Bolivia. When she starts to go inside, he tells her that the protocol is already in effect. They watch as the opera house is filled with gas that embeds the structure in amber.
Broyles, Charlie, and Lincoln return to Fringe Division in New York City and check in with Agent Farnsworth, who is running scenarios. The high probability is that she'll try to leave the country. A report comes in that Olivia was at the opera house and left in a taxi, and Broyles orders a check of taxis.
Olivia tells Henry to keep driving. He gets a call from his wife and he chats with her. When he hangs up, he asks her if she has someone and she admits her someone is Peter, and he helped her get her there. Olivia then tells her to head for Massive Dynamic's address, and Henry stops for gas first. Olivia goes into the restroom and checks the tattoo on her neck, and then goes into the stall to cry. Outside, Henry contemplates the photo of his family.
Olivia comes out and finds Lincoln waiting for her. He believes that she's his Olivia and tries to convince her to surrender and come with him. She draws a gun and tells him to drop his gun, and he reluctantly does so. Olivia insists she's not who he thinks she is, and he kicks the gun over to her. Lincoln warns her that she can't keep running, and Olivia locks him in the bathroom. She goes to the taxi as more Fringe agents pull up. She opens fire on them and tells Henry to get in the car. When Charlie comes running up, she shoots the valve on the propane tank behind him, knocking him down and covering their escape. As they go, Henry notes that Olivia is a hell of a shot, and she realizes that she's not. He then pulls out the tracking device in his cab and tosses it out the window.
Broyles reports to Walternate that Olivia has gotten rid of the cab's tracker. Walternate replays the footage and notes that only one person could have made a shot like that. He believes that their memories treatments are working.
Henry drives Olivia to the address she requested, but she realizes that there's nothing there but a park, because it was never built. She gets out and looks around, and realizes that she's stuck. Henry asks if she's okay, and Olivia asks her to take him to a safe house in Tarrytown that she's suddenly remembered.
Charlie comes to see Frank Stanton, Bolivia's fiancé.
As they drive, Henry notes that Peter must be important to her. She thinks he's talking about Frank, and she corrects herself.
Frank admits to Charlie that he hasn't slept since Olivia was injured. Charlie promises to find her, and asks him if he can think of anyone else she might have gone to for help. Frank tells him that Marilyn is back in town.
Henry arrives in Tarrytown and offers to wait for Olivia. She tells him to go home to her family, and admits that the only way she can prove she's not crazy is to tell him some crazy things. Henry admits that a few years ago, he had problems and Jasmine believed in him and the man he knew he was. He tells her that sometimes you have to believe what you can't see. Olivia thanks him and gets out.
As Henry drives away, Olivia goes up to the house and rings the doorbell. No one answers, and Olivia goes around to the back and slips in through a window. When she hears music, Olivia draws a gun and goes inside, and finds a dog in the kitchen. On the mantle, Olivia finds photos of herself as a child... and her mother Marilyn. Marilyn comes in behind her and calls her by name. She embraces Olivia and explains that she came home as soon as she heard that Olivia was having problems. Olivia tries to explain that she's not her daughter and she's never been there. Marilyn asks how she knew to come there, and Olivia starts to remember painting with her. Olivia starts to accept that she's the alternate Bolivia and embraces her mother.
Charlie arrives and asks Marilyn if she's heard from Olivia. Marilyn ushers him in and Olivia greets him.
Walternate tells Agent Brandon that his plan was sound but just needed a little more time to work. Brandon realizes that it was the adrenaline from her escape that triggered the lymphocytes from Bolivia that they injected into Olivia.
As Olivia leaves with Charlie, Henry watches from his cab. He then drives away.
Olivia thanks Charlie for being her friend, and he thanks her for not shooting him.
Walternate tells Colonel Broyles to give Olivia the weekend. He wonders why Walternate is putting Olivia on his team, but Walternate refuses to answer.
On the "real" Earth, Peter reports to Senator Dennis Van Horn about his experiences on the other side. The senator has one more question: why did Peter come back rather than stay and sabotage Walternate's efforts. Peter doesn't answer.
Outside, Bolivia is talking with Walter when Peter comes out. He suggests they go for dinner, and Peter admits that he couldn't stop thinking about her. He kisses her and they leave.