At the Harvard lab, the team examines Michael and confirms that he doesn't have any tech and apparently never had any. Olivia tries to convince Michael to talk to them but he remains silent. Walter suggests that they try to enter Michael's mind like they did with September and enthusiastically offers to shoot the boy up with drugs. Peter and Olivia refuse and Walter snaps at them, irritated that they're not following his advice. As he storms off, Olivia wonders why Michael isn't responding to them when he did in the original timeline.
Nina is working in her office when Olivia calls her on her private line. As the assistant notices that the call came in on Nina's private line, Nina tells Olivia that it's not safe and that she'll call her adopted daughter back in ten minutes.
A few minutes later, Windmark and his Observer squad arrive and enter Nina's office. She's not there and Windmark asks the assistant where Nina went. The assistant admits that she doesn't know and that Nina received a private call twenty minutes ago and then took an early lunch. Windmark explains that a sublimation device has gone missing from the Ministry and has his Observers hook up a device that picks up residual sound waves from the office's glass window and listens as Nina mentions a child Observer.
Nina meets Walter, Peter, Olivia, and Michael on a street and assures Olivia that she's glad to help. Michael doesn't respond to Nina, who offers to take them to a secret Massive Dynamic "black lab" with equipment they can use to communicate with Michael. As they go, Nina privately asks Peter how Walter is doing and Peter admits that Walter is vacillating between his original ruthless self and his post-brain-surgery version. Nina admits that she agreed to remove the pieces of Walter's brain once he completed his plan, but admits that Walter may regress to the point where he no longer wishes to have them removed. As Peter catches up to Olivia, he sees her studying one of the Etta resistance posters.
Windmark realizes that Nina isn't returning and leaves for the warehouse storage facility where the sublimation device was stored.
Nina takes the group into the black lab and Olivia stays with him while Nina shows Peter and Walter the main laboratory. One cylinder contains a dead Observer and Nina explains that they Resistance used the lab to study the Observers in an attempt to understand how they communicate among each other. She proposes that they use the same equipment to communicate with Michael, and Peter goes back to get the boy. He comments about how Olivia was looking at the resistance poster earlier and they both admit that they still think of their daughter every time they see a poster.
Once everyone has gathered, Nina explains that the Observers' brains work differently and places an ecog halo on Michael's head to serve as an electro-cognitive translator. The device translates Observer thought patterns into images that humans can understand. Walter tells them to prepare "the subject" and Peter reminds his father that they're dealing with a boy, Michael.
Windmark goes to the warehouse and one of his loyalist officers informs him that Nina's comm device is off-line. The Observer then interrogates the head scientist, Roe, informing him that Nina is a traitor. Roe insists that he has no idea where Nina is. Scanning his mind, Windmark is satisfied that the human is telling the truth.
Once Peter has placed the ecog halo on Michael's head, Olivia assures Michael that they'll stop if he indicates he's uncomfortable. They ask him about Walter's plan and his part in it, but Michael doesn't respond and Nina discovers that Michael's brains work differently than the Observers that they studied. When Olivia notes that Michael formed an empathic connection with her in the alternate timeline, Nina speculates that since Michael no longer has that connection, he can't communicate with them. To reestablish the empathic connection, they will have to let Michael into one of their minds. Walter agrees but Nina warns them that they will need to get a second ecog halo while she reprograms the software. She gives Olivia the number of her inside man, Darryl Hastings.
At the warehouse, the Observers gather the staff and have them wait in line for interrogation. Hastings receives a call and ignores it.
Outside, Olivia, Peter, and Walter pull up to the warehouse and Olivia tries and fails to reach Hastings on her comm. They try to get through the security lock but realize that they need Astrid's help and call her at the lab.
The Observers bring Hastings into the interrogation room and he explains that he is only indirectly connected to Nina.
Astrid tells Peter how to wire the lock and he uses a device to short it out. Once it blows out and the door opens, the trio goes inside.
Windmark realizes that Hastings is lying and has his men restrain the engineer to his chair.
The team enters the warehouse and uses a terminal to find a second ecog halo. Once they locate it, Walter confirms the case holds what they need. As they prepare to leave, Olivia spots Windmark and Hastings in the interrogation. Meanwhile, Windmark continue to telepathically probe Hastings, forcing him to admits where the fugitives are. Hastings finally confesses that he sympathizes with them but he has no idea where they are.
At the lab, Nina asks Michael to stay in the lab. She then goes outside to get a clear signal to call Hastings. When she does, the loyalists trace her comm signal. She then gets a call from Olivia, who warns her that Hastings may have compromised her location. Nina tells Olivia that she's fine, hangs up, and destroys her comm. Olivia and Peter watch the interrogation room and see Windmark and his Observers teleport away. Taking advantage of the opportunity, the Fringe team breaks into the room, kills the guards, and frees Hastings. The tortured Hastings tells them that Windmark has located Nina.
Nina goes back to the lab and finds Michael without the ecog halo. As she starts to reassure him, he touches her face and she stares at him in surprise and shock. After a moment he lets go and looks at the monitors. Windmark and his men are pulling up outside and Nina tells the boy to come with her.
Peter and the others drive back to the black lab but run up against a checkpoint. They have no choice but to abandon their car, sneak into a parking garage, and steal a van.
Windmark and the Observers teleport into the underground lab and begin searching the place. Nina is calmly waiting for them and Windmark demands to know where the fugitives are hiding. She tells them that they're long gone and Windmark warns her that she won't be able to hide her thoughts for long. As his men search the lab, Windmark finds the cylinder with the dead Observer and turns from it in disgust. He dismisses Nina as an animal and starts scanning her mind, and sees the image of Michael in her thoughts. Nina tries to distract him, asking why he's so concerned about the boy, and Windmark explains that Michael is a genetic anomaly, XB-6783746. The boy is from the Observers' future and was scheduled for destruction, but disappeared until now.
The loyalists report no sign of the fugitives and Windmark prepares to extract the memories from Nina's mind. When he notices that she's not frightened, Nina explains that she has studied the Observers' physiology and confirmed that they have regressed and developed primitive instincts that humans have grown beyond. Humans are now evolutionarily superior to the Observers and Nina dismisses Windmark as an animal. As Windmark has his men restrain her, Nina grabs one of their guns and aims it at Windmark. He smiles and says that she can't hurt him, and Nina says that she knows... and shoots herself in the head.
Sometime later, Peter, Olivia, and Walter arrive at the lab and find Nina's corpse. Walter goes to it and takes his old friend's hand, while Olivia gently covers Nina over. Peter notices the surveillance cameras and reviews the footage, which shows Michael touching Nina and then leaving with her. They fast forward the video and confirm that Windmark never found Michael, and conduct their own search. They find Michael hiding inside the cylinder beneath the dead Observer. He goes to Nina and, looking at her corpse, sheds a single tear.
The team takes Michael back to Harvard and Walter links minds with the child Observer. They confirm that Michael can now understand them and they ask if Michael knows why he's a part of Walter's plan to defeat the Observers. Michael removes the ecog halo and touches Walter gently on the face, triggering a rush of memories. Walter finally sees a memory of the man he knew as Donald: September, as a human.