At Harvard, the Fringe team cannot communicate with Michael the Observer child. The empathic connection he had with Olivia in the other timeline is gone. Walter is cranky and impatient, more like his old self than ever.
Olivia contacts Nina Sharp, who leaves her Ministry of Science office to call back in private. Shortly afterward, Captain Windmark and two Observers arrive. They know the Ministry gave the fugitives a sublimation device. Using special tech, they re-create what Nina said on her comm and hear the phrase "child Observer."
Nina leads Walter, Peter, Olivia and Michael to an old Massive Dynamic "black lab," now used by the resistance. Stored inside are several Observer bodies used in experiments, which they cover before bringing Michael in.
Nina thinks they can use a helmet-like device called an Electrocognitive Translator (a/k/a Ecog) to get into Michael's mind, but it turns out that his mind isn't like other Observers'. Nina realizes they need to let Michael get into their minds instead. This requires another Ecog halo, which is at the Ministry.
Nina stays with Michael while the others (with remote help from Astrid) sneak into the Ministry archives . . . where Windmark's investigation is underway. Dr. Hastings, who helped them with the sublimation device, struggles but fails to resist Windmark's mind probe. By chance, Olivia catches sight of the interrogation.
Meanwhile, Nina comes out of the lab to call Olivia, since her comm doesn't work underground. Loyalists trace the signal. Olivia tells Nina she's been compromised. Deeply shaken, Nina goes back inside.
When Olivia and Peter see Windmark and his men suddenly teleport away, they burst in and save Hastings. He tells them the Observers know where Nina is.
In the lab, Nina is crying but tells Michael it's OK. He touches her face and, amazed, she says, "Oh, my God." The surveillance feed shows Windmark and crew outside. She tells Michael to come with her.
Alone, Nina calmly greets Windmark and his men. She resists his attempts to read her, but he says that won't last. He uncovers an Observer body and snarls, "You . . . animals." He informs Nina that Michael is no child: he's a genetic anomaly, designate progeny XB-6783746. Like all anomalies, he was scheduled to be destroyed, but he went missing. No one knew what became of him - until now.
Windmark wonders why Nina isn't frightened. In her trademark cool, logical tone, she informs him that the reason Observers tilt their heads that way is because it's an involuntary reflex in their physiology, one very much like a lizard's. She adds that lizards, for all their evolution, are incapable of love, of dreaming, of contemplating beauty - of knowing something greater than themselves. Not unlike Windmark's kind. The resistance's experiments showed that, for all the Observers' years of evolution, they inadvertently honed primitive instincts that humans surpassed long ago. So in reality, Windmark is the animal.
Windmark tells his Loyalists to restrain Nina for a deeper probing. She takes the gun from one and points it at Windmark. He says she cannot hurt him with that. "I know," she says.
And Nina shoots herself in the head.
Walter, Peter and Olivia are devastated to find Nina's body. The surveillance video reveals that she sacrificed herself to protect them, the plan and the boy. Olivia finds Michael hidden beneath one of the units holding an Observer body.
Michael approaches Nina's body and sees Walter weeping. The boy is crying too.
Back at Harvard, Michael puts his hand on Walter's face, as he had with Nina. We see a flood of images - Walter's memories, including their first encounter with the boy. "The boy is important," says September the Observer in the flashback. "He has to live." Then we see Walter greeting the man whose identity has been such a mystery . . . and who is suddenly so familiar.
"I know who Donald is," Walter says. "Donald is September."