At Harvard, the Fringe team tries to work out where Michael is, since Astrid has been unable to track them via overhead satellite. Walter is concerned that they can't contact Donald, since he didn't give them a way to reach him. Olivia calls Broyles at Fringe headquarters for help and tells him that they need to find the boy. Broyles talks to a loyalist lieutenant and claims that Windmark authorized him to provide additional security but neglected to give him the location where he had to send his men. The lieutenant is concerned about the recent infiltrations involving the resistance leader known as "The Dove," but Broyles convinces him to tell him that Michael is being kept at the Liberty Island facility.
At Liberty Island, Windmark interrogates the captive Michael, who remains silent. Windmark tries to read the boy's mind but only hears the echo of his own questions. When he probes deeper, his nose starts to bleed and the captain wipes away the blood. When he probes further, his eyes start to fill with blood and Windmark tells the scientists to run diagnostics and find out what the "anomaly" is.
Broyles contacts the Fringe team on a scrambled line, sends them a schematic of the Liberty Island fortress, and warns them that the security is the best in the world. Olivia suggests that rather than try to get through the security, they bypass it entirely by going to the Other Side, traveling to Liberty Island, and then transitioning back over. Astrid points out that Olivia's ability to transition because of cortexiphan treatments were lost when the drug burned out of her system, Olivia suggests that she could get her abilities back and Walter admits that it's possible.
As the team gets out cortexiphan from storage, Walter explains that Olivia's neural pathways were permanently altered and a dose of cortexiphan could reactivate them. However, he warns that the procedure is uncertain, and Peter is concerned that the treatment could kill his wife. Olivia points out that they have no other options and Peter reluctantly agrees, but wonders how they can know if the Other Side is safe or even still exists. Astrid suggests that they use Walter's dimensional window to find out.
The Observer scientist gives Michael a paralytic to hold him still as they scan his body. Windmark, watching, is still dealing with a nosebleed and finally tells the scientist to send him a report when he has information.
The Fringe team drives to Battery Park and sets up Walter's dimensional window. When they look through it, they see people casually walking through the park on the Other Side, and an intact Statue of Liberty in the distance. Satisfied that the Other Side is safe, the team prepares to go ahead with their plan.
Donald slips into the Harvard lab through the air vents. When he discovers that no one is there, he starts distilling a liquid from the crystals that he's gathered and placing it in glass cylinders.
The team contacts Alin and he sends them to a safehouse with medical equipment. The field surgeon, Tobin, provides Walter with the equipment that he needs. Walter gives Olivia the first of four cortexiphan injections directly into her brainstem. Her heartbeat and blood pressure rise precipitously and Tobin warns that she's in danger. Walter insists that he's the leading authority on cortexiphan treatments and gives Olivia a second and third injection. When Peter says that they have to stop, Walter explains that Olivia will have to transition four times so she needs four injections. He asks his son to trust him and then gives Olivia the final injection.
The Observer scientist and his assistant examine the completed scans and are surprised to discover that Michael's neural system is vastly different than an Observer's. It gives him both enhanced intellect and emotional responses.
As Olivia rests briefly, Peter and Walter discuss the sacrifices that they've made. Walter considers telling Peter the sacrifice he must make to save the world but at the last minute decides not to. Meanwhile, Olivia's mind is blurring in and out of reality. Walter wakes her up and sees them appearing and disappearing as her vision flickers between Their Side and the Other Side. Walter tells her that she will have three hours at most and gives her a watch set to count down the time. He also warns her that if her jumps burn up too much cortexiphan in her systems, she'll start to suffer withdrawal symptoms. If that happens, Walter tells Olivia to jump back immediately.
The team drives to the ruined building that stands in the same spot as Fringe Division on the Other Side. As Peter walks there with his wife, he figures that she'll make it back with Michael because they have to succeed and recover Etta by resetting the timeline. They kiss and then Peter steps back and watches as Olivia jumps over. Fringe Division quickly detects the breach between worlds and sends soldiers to investigate. Olivia goes to Fringe Division and surrenders herself.
Bolivia and her husband Lincoln, twenty-one years older, are notified and come to see Olivia in their office. Olivia has found a photo of the two of them with their son. When they come in, she explains how she spent twenty-one years in amber. They hug and Olivia explains why she needs their help. As they talk, Olivia hallucinates a young version of Etta in the room watching her. As they hit the two-hour mark, Lincoln goes to prepare transport to Liberty Island while Bolivia asks if Olivia is doing okay.
Donald continues building the wormhole generator, inserting the liquid cylinders into the device. He activates it but watches in horror as the power levels drop to a bare minimum.
Windmark travels to 2609 to tell the Commander what they've discovered about Michael. The captain is clearly disturbed as he warns his superior that the resistance plans to use Michael to destroy them. The Commander says that what is important is understanding what the anomaly is, and tells Windmark to have the boy dissected and the pieces studied carefully.
As Bolivia goes off to compare their schematics to the ones that Broyles provided, Lincoln talks with Olivia and assures her that Walternate is still alive but retired, and lecturing at Harvard. When he hesitates, Olivia assures him that she's fine with his choice to marry her counterpart and tells him that he deserves all of the happiness that he has. Bolivia returns and they go to the room that corresponds to the lab where Michael is being kept. The couple wishes her luck and Olivia transitions over into the lab. Michael has been taken to an operating theater and Olivia goes to find him. Her vision grows increasingly blurry as her perceptions see both worlds at once and then neither. She manages to spot an Observer coming after her and makes it to the security room. After killing the guard, Olivia finds Michael on the monitors. Another Observer teleports in and attacks her, but she manages to kill him as an alarm goes off.
An Observer teleports into the operating room and tells the Observer surgeon to stay there and protect the boy. After he leaves, Olivia slams through the doors, kills the Observer, and tells the nurse to back away. As she helps Michael up, he smiles at her. As the Observer returns, Olivia jumps back to her world and the Observer follows her. He attacks Olivia but Bolivia and Lincoln arrive and shoot him a dead. A second Observer teleports across and they dispose of him as well. Bolivia takes Olivia and Michael to the boat and they cross to Battery Park. She wishes her counterpart luck and then watches as Olivia jumps back to her own world.
Windmark is in his office writing down the same words repeatedly when two of his assistants bring in the loyalist lieutenant. The captain points out that the lieutenant was one of only three men who knew where Michael was being kept, and asks if he told anyone. The lieutenant admits that he told Broyles after the director told him that he had authorization from Windmark.
Donald visits a former comrade: December, one of the other 12 Observers sent back to observe human history. He reminds December that Observer owes him and he's there to collect, and December reluctantly lets him in.