At the lab, Peter, is cutting into the amber when a light flashes briefly through the windows. Once the security team passes, Peter goes back to work until he hears Walter come in behind him. Walter apologizes for startling him and tells his son that he needs his rest. Peter insists that they need to get the tapes, and Walter suggests that they recover his memory of September by using the sensory deprivation tank.
Olivia and Astrid give Walter a sedative and put him into the tank. His vitals start to rise as Walter remembers. He finds himself in an apartment, the same one that he saw the human September in. Walter looks around and finds September, a frozen memory, and then looks out the window. He sees the Empire State Building and realizes the apartment is under the bridge. Once they get Walter out of the tank, they confirm it's the Williamsburg Bridge. Walter figures that September is still alive and says that they must hurry. He goes off, whistling
Windmark is in his office listening to their recording of Nina's conversation about the child Observer. His lieutenant comes in and says that "he" is waiting for him. Windmark tells his lieutenant to continue the search for the fugitives and teleports through time to Manhattan in the year 2609.
Walter, Olivia, and Peter take Michael and drive to the apartment location. Once he confirms which apartment he was seeing the view from, Walter runs off and Peter goes after him. When Peter wonders why he's acting so wildly, Walter insists that he's doing fine. He tells Peter that it's no longer necessary to remove the pieces of his brain that were causing him to revert. When Michael touched him, Walter explains that everything he thought he knew was meaningless. He also remembered things that he hasn't experienced, from the other timeline before Peter was erased. Walter describes some of the things they experienced in the other timeline. Peter wonders how Michael could do all that and Walter admits that he doesn't know. However, he still doesn't remember the plan and they wonder why. Walter tells his son that he loves him more than ever and they embrace.
In 2069, Windmark meets with the commander and informs him that they have met the anomaly, Michael, in 2036. He believes that someone insured Michael's survival because they thought it was important.
Walter finds the window he looked out of and they go upstairs and ring the door. No one answers and Walter tries knocking. Donald/September finally comes to the door and greets Walter by name. Walter explains that they were trapped in amber for 21 years and Donald goes to Michael. After a moment, the boy holds up his hand and Donald takes it. They go inside and explain to Donald how they found him, and Walter asks what happened to him. Donald explains that his people apprehended him and removed his device as punishment for interfering in the timeline. The Observers experimented on him, conducting "biological reversion" and turning him back into a human. Donald admits that it wasn't much of a punishment to him, and he chose the name Donald after Donald O'Connor because the first movie they watched was Singing in the Rain
. When Michael grows restless, Donald plays Greensleeves
on a music box and the boy gets up and winds it on his own. Donald tells the others that Michael was created in the future using designated material from a donor. A scientist rewired the part of the brain that caused jealousy, generating increased intelligence but sacrificing emotions. The process created the Observers and more emotions were abandoned. The Observers lost perspective of the value of all emotions, good and bad, and new reproductive procedures were conceived when romantic love was eliminated.
Windmark goes to one of the breeding labs and requests information on the Michael anomaly.
Donald explains that Michael's brain had developed differently from other offspring. His maturation was halted and he was considered a defect. Donald was familiar with fatherhood from his time in the 21st century and he took Michael to the past where he would be safe.
Windmark confirms that the donor was September, one of the original twelve Observers who traveled back in time. The Commander wonders why September would protect a genetic defect and Windmark asks for a protocol suspension so he can go back and eliminate the resistors at the moment of conception. His superior refuses, saying they don’t want to deal with a change in probabilities, and reminds Windmark that they have calculated a 99% plus chance of success. Windmark points out that Michael had less than a one percent chance of existence and yet he did, and the Commander asks if there is something wrong with him. The captain admits that the idea of destroying them consumes him, but the Commander dismisses the resistors as inconsequential.
Donald explains that Michael is more than just an Observer. His empathic abilities developed further and his intellect functions on a level that none of them can understand. Walter realizes that Michael is a hybrid, and Donald tells them that the turning point was February 2, 2167, when they developed the process to remove emotions to increase intellect. He wants to send Michael to that point in time and give the scientists living proof that they don't have to sacrifice emotion for intelligence... eliminating the Observers from the timeline. Walter realizes that was the plan they were working on before he went into amber. Donald explains that once he lost his implant, he went to Walter and they tried to work out a way to send Michael forward in time to 2167.
Peter tells Donald what they've gathered and the ex-Observer says he can help them decipher the scrolls. Upset, Olivia leaves the room, while Donald tells Walter that the device will give them time travel, and he has hidden tech he stole from his time to power the device.
Peter goes out to the kitchen where Olivia is getting a glass of water. She tells her husband that when they reset time, they will get Etta back. Peter isn't convinced and warns Olivia that they still have a long way to go.
Windmark returns to his office and receives a report on how September was captured when he was obtaining rocks from a mine in Pennsylvania. He was questioned, tagged, and released, and Windmark tells his assistant to initiate the location protocol and find Donald's address. The Observers teleport in a few minutes later but no one is there. They search the apartment and find the locator chip in the sink. Windmark confirms that the coffee is still warm and tells the loyalist to review the security cameras in the area. He then goes into the next room, unwittingly setting off a sensor. Windmark looks at Donald's belongings and souvenirs, and then turns on a player with recorded jazz and listens in confusion.
As they arrive at a storage facility, Donald gets video from the sensor confirming that the Observers are there. When Walter says that he can't go back, Donald tells him that there is no "back there" to go to.
When Windmark's lieutenant comes in, the captain notices that his foot is tapping in time to the music. The Observer stops it from tapping... and Windmark sees the sensor on the wall above the door turn red. They teleport out just as an anti-matter bomb destroys the apartment. Loyalist troops arrive and show Windmark video they found of the group and the van. Windmark confirms the video was taken 14 minutes ago and tells the loyalists to set up a perimeter.
Donald and Walter go into the storage shed and find the tech that Donald placed there. Walter explains that Michael communicated to him when he touched him, giving him awareness of the other timeline. He reminds Donald that he said, "The boy must live" and realizes that he was referring to Michael, not Peter. Walter also says that Michael showed him that Walter would have to sacrifice himself for the plan to work. Donald admits that it's true and asks if Walter is frightened, and Walter admits that he is. He wonders if Michael showed him all the other experiences so that he'd know that he has he has loved and come to terms with why he did it. Donald admits that he doesn't know and tells Walter that he himself chose to do it to make amends for all the damage he had done in the past.
The former Observer asks Walter if he remembers getting a white tulip. Walter does and figures that it was a sign from God. Donald then removes a hidden brief case and explains that he took the tulip from the other timeline and kept it. He knew the symbol of the white tulip would give him the strength to carry on when he doubted that they could succeed. Walter admits that he could use the tulip and Donald says that only Walter knows what happened to it.
The two men take the technology to the van and Donald says that there are a few things he will have to get before they can complete the plan. He extends his hand to Michael and promises that he will see him again. Donald starts to walk away and Michael looks after him for a moment.
As they drive out of New York City, they spot a roadblock up ahead and take a side alley. Olivia calls Astrid and has her access the resistance network and check the local feeds. Astrid confirms that there's no way out. The team abandons the van and Astrid directs them to the monorail where there's a hole in the perimeter. Peter tells them to wait and then goes back to the street to confirm that the loyalists have blocked off their route with another checkpoint. Olivia says that they'll split up and takes Michael with her, posing as a mother and child.
Once Olivia and Michael pass the checkpoint on foot, a loyalist hummer pulls up, cutting off Peter and Walter. They duck back into the alleyway and after a few moments, the hummer moves on. As Walter and Peter head for the monorail, Olivia and Michael get there first. Peter calls and says that they're not far, and will meet her at the train. Olivia and Michael get onboard and spot Peter and Walter approaching. However, they're forced to turn around to avoid an approaching loyalist patrol. They get into a car further down while the patrol enters Olivia's car and start searching. Michael gets off the train just as the doors close. The loyalists immediately find him, confirm who he is, and take him away as the monorail leaves the station. Windmark is waiting outside and studies Michael carefully when the loyalists bring the boy to him.