Late at night in the Harvard lab and Peter is keeping occupied himself cutting open more of the amber when Walter comes in. Walter admits that he couldn't sleep either and tells Peter to get some sleep. Peter insists that they need the rest of the tapes that explain the plan and Walter suggests that he go into the sensory deprivation tank to regain his lost memories of September.
The next morning, Olivia and Astrid get Walter into the tank and give him a sedative. They monitor his vitals and they start to go up as Walter remembers the past. He describes how he's in the human September's apartment within his own memories and looks out the window. Once Walter describes what he's seeing, they confirm that he's somewhere near the Williamsburg Bridge in New York City. Walter figures that September is still alive and living there, and goes off whistling.
At the Observer district house, Windmark is listening to a recording of Nina's conversation about Michael when his lieutenant comes in. The lieutenant informs hit hat their superior is ready to see Windmark and the captain teleports out of the room... and to Manhattan in the year 2609.
While Astrid remains behind, the others take Michael to the apartment address that Walter saw in his memories. When they get there, Walter eagerly runs ahead and Peter goes after him, asking what's wrong. Walter explains that since Michael touched him, he not only regained some of his memories but learned that what he knows is meaningless. Michael also showed him experiences that Walter went through in the other timeline, the one that existed before Peter was wiped from existence. Peter wonders how Michael could have done that and Walter admits that he doesn't know. However, he still doesn't remember the plan, but he assures Peter that he loves him more than ever and hugs him.
In 2069, Windmark meets with the Observer Commander and tells him that they have found the hidden anomaly, Michael, in 2036. He believes that someone hid Michael in the past and made sure that he survived because they believed that the boy was important.
Walter pinpoints the window that he looked out of in his memories and they got to the door. September, now a human being, finally opens the door and is surprised to see Walter there. Walter explains that they were forced to trap themselves in amber to avoid capture. Donald goes to Michael and the two of them touch hands, and then they go inside. The Fringe team explains how they found Michael and Walter asks what happened to Donald. The former September explains that his people apprehended him after he interfered in the timeline, stripped him of his implant, and put him through "biological revision" as punishment. Donald admits that he doesn't consider it punishment because he has always valued humanity, and that he chose the name Donald after actor Donald O'Connor in Singing in the Rain.
Michael nervously gets up from his chair and Donald plays a bit of Greensleeves on a music box. The boy continues playing it, calming down, and Donald explains that Michael was created in the future using designated genetic material. On February 2, 1967, a Swedish scientist developed a procedure to rewire the human brain, removing jealousy to make room for heightened intellect. When the procedure was used, it created the first Observer and scientists continued making further modifications, removing more emotions and accelerating intellectual development. The Observers that were created decided that all emotions, good and bad, were simply distractions and got rid of them. When romantic love was eliminated, other means were found to reproduce.
In 2609, Windmark goes to the reproduction lab and asks an Observer scientist for information on the Michael anomaly.
Donald explains that Michael developed differently from the other Observer offspring. The scientists halted his maturation and designated him a defect. Donald, who as September had witnessed fatherhood in the 21st century, understands the concept and came to have the same feelings for Michael. He then rescued Michael and took him back into the past where he believed that the boy would be safe.
Windmark confirms that September was the donor who provided Michael with genetic material. He returns to the present and informs the Observer Commander that September was one of the original twelve Observers who traveled into the past. Windmark asks for a protocol suspension so that he can go back in time and eliminate the fugitives before they can begin their plan. The Commander refuses, saying that they don't want to risk a change in their calculated probability of success. When he reminds Windmark that they have calculated an all but 100% chance of success, Windmark reminds him that Michael had almost no chance of surviving. The Commander asks if something is wrong with him and Windmark admits that he is consumed with the idea of destroying the fugitives that have opposed him. The Commander looks at him suspiciously and then tells him that the fugitives are inconsequential to their plans.
Donald tells the others that Michael has empathic abilities and an intellect that functions at a level that none of them can understand. Walter realizes that Michael is a hybrid, and Donald explains that their plan was to send Michael to the scientists in 2167 before they began removing emotions. He hopes to give the scientists living proof of what their experiments will ultimately cause, and show them that there is a better way. If their plan succeeds, the Observers will never exist and will never invade 21st century Earth. When Donald lost his implant, he went to Walter and they tried to work out a way to create a time machine so they could send Michael to 2167. Peter tells Donald which pieces that they've gathered and Donald says that he can help decipher the scrolls.
Olivia, shocked, takes in everything that Donald has told them and then goes into the kitchen. Meanwhile, Donald tells Walter that he has additional Observer tech hidden away that is a vital part of their plan to create the time machine. Peter goes after his wife, who points out that if Donald and Walter's plan succeeds, they will have Etta back because the Observers never invaded and caused her death. Peter is skeptical that it will work and warns Olivia that they soon have a long way to go before they can find that out.
Windmark goes back to his office and reviews September's record. He confirms that the Observer was arrested at a mine in Pennsylvania, tagged, and released after questioning. Windmark tells his assistant to activate the tracking chip and they soon find out where Donald is living. They teleport there but discover that the fugitives and Donald have just left. The blood-covered locator chip is in the sink and the Observers realize that Donald has given them the slip for the moment. Windmark goes into Donald's study, unwittingly activating a sensor, and looks at the ex-Observers belongings. He finds a player and turns it on, and jazz music fills the room.
As the team arrives at the storage facility, Donald receives a video feed from his apartment and warns the others that the Observers are there. Walter warns him that he can't go back and Donald tells him that there is no place to go back to.
Windmark's lieutenant comes in and the captain is puzzled when he notices the Observer is tapping his foot to the music. Windmark looks up and finally notices the sensor above the door. As it turns red, Windmark and his lieutenant teleport out just as an anti-matter bomb activates, destroying the apartment. Loyalist troops arrive and inform Windmark that they've spotted the fugitives on the security cameras. The Observer tells them to set up a perimeter and capture the fugitives.
Donald and Walter go into the storage shed and recover the hidden Observer tech. Walter tells Donald what happened and realizes that when Donald saved Peter and said, "The boy must live," he was referring to Michael, not Peter. Walter explains that when Michael touched him, the child Observer showed him that as part of the plan, Walter would have to sacrifice himself so that it would succeed. Donald admits that it's true and asks if Walter is frightened. Walter admits that he is and wonders if Michael showed him the alternate timeline so that he would know that he has loved, and so he could come to terms with his past. Donald admits that he doesn't know and explains that Walter deliberately made the decision to sacrifice himself so that he could make amends for the damage he had caused in the past.
As they prepare to leave, Donald asks Walter if he remembers the white tulip. Walter does and says that it's his sign from God, a symbol of hope. Donald takes out the empty envelope and explains that he knew it would give Walter the strength to carry on when he had doubts. When Walter asks if he has the tulip, Donald admits that he doesn't and that the last time he saw it, Walter had it. As they leave, Donald tells the others that he will have to go to recover a few more pieces of tech to complete the plan. He promises Michael that he will see him again and leaves.
As the Fringe team leaves, they spot a checkpoint up ahead and pull off into an alleyway. Olivia calls Astrid and has her accesses the security cameras by remote, and she warns them that the loyalists have surrounded the area. As the team abandons the van, Astrid finds one gap in the perimeter at the monorail station. Olivia and Michael go ahead first to avoid attracting suspicion and get past the checkpoint on foot. Peter and Walter are forced to stay behind when a loyalist hummer pulls up. By the time they catch up, Olivia and Michael have already reached the monorail station and entered a car.
Loyalist patrols are searching the station and Peter and Walter are forced to get into a car further down the train from Olivia. More loyalist guards approach Olivia's car and she realizes that they will quickly find her. Michael steps out through the doors as they close and approaches a patrol leader. As Peter and Walter catch up to Olivia, they can only watch as the train pulls out of the station. Meanwhile, the loyalists take Michael to Windmark, who studies the boy with great interest.