After the shocking kiss, Peter is trying to make sure that Olivia is alright. She seems to be back to normal, though her instincts told her to kiss him. She passes it off as residual effect of their last mission, but Olivia can't ignore the migraines and the flashes of memories once Peter has left.
At the Deerfield Mental Hospital, a patient tells an empty room that it is time. The scene switches to Douglasville, New York, where several men are breaking into a house. The mental patient is giving the burglars directions through the house, when one of the attendees pulls him away. It doesn't stop the three men from going after the man in the house and attacking him. As the man fights back, the mental patient goes into a severe fit. But once he is dead, it all passes away.
This case attracts the Fringe Division, so they go to the mental hospital. The nurse contacted the police after hearing the murder that her patient Sean described in detail. The young man was known for having these fits before and had been in such institutions since he was 14. As the nurse tells them all this, Olivia is caught off guard by other visions of her and Peter walking through a mental hospital.
As they interview Sean, he is much more calm than before. He also doesn't understand how the voices in his head were behind this man's death. His filled with voices, and last night heard three. One voice per attacker, which seems to also relate to all his other fits. He would appear to be hearing the thoughts and voices of other people according to Walter. After telling Sean to stop taking his medication, Walter confronts the nurse for the misdiagnosis of schizophrenia. She is overwhelmed by Walter telling her that the voices are all real, but accepts it all the same.
The nurse leads Olivia to explain this to the other doctors, but she isn't seeing this mental institution. In her mind, she is seeing her past self and Walter first visiting Walter when he was in the mental hospital.
After this, Olivia visits Peter at his home. She is able to remember more about his time line, retelling another case and more intimate memories with Peter. She's remembering everything. Hearing all this terrifies Peter.
He forces her to go to Walter so he can make sure she is okay. During all this, Olivia reminds Walter and Peter that she isn't scared of anything that is going on. However, she can remember how things happened in their time line. They are fuzzier memories than the ones from Peter's time line. Walter explains it as Olivia's psyche empathizing with Peter and his desire to have his own Olivia back. It's not the perfect explanation, but Walter appears to be thinking up another explanation. The thought escapes him though.
When Lincoln arrives with the updates on their case, he and Peter must take a step back from worrying over Olivia. They have found DNA from one of the men who broke into the house, and Walter notices that both the attacker and Sean have the same type of mark on the DNA and thus must be related. He hypotheses that the DNA link is why Sean can hear their thoughts. Ignoring her faltering mind, Olivia heads out with Lincoln to question Sean's mother. As she leaves, Walter places the blame for Olivia's condition on Peter.
She doesn't understand what is happening to her son, but does have information as to Sean having brothers. He was from in vitro fertilization, and so can point Olivia and Lincoln towards the sperm donor. It turns out that Sean's mother was called earlier by the same man who was killed because he was writing an article about IVF.
Astrid is keeping an eye on Sean, who is hearing some of the voices as they eat. He can't understand what they are saying since there are far too many in his head.
Back at the lab, Walter is examining strands of Olivia's hair. While making tea, the honey sparks an idea. Olivia is at a dead end from learning about the IVF clinic and the sperm donor. As Peter comes to help, she notices a scar on her hand that she doesn't remember. It is more recent, but that doesn't stop Olivia from holding onto his hand. An annoyed Walter interrupts their moment to inform the two about his breakthrough.
Bees. Their system of communication is similar to what they are seeing with Sean, and do so to protect the hive. Walter thinks that this is what happening with Sean and his half-siblings. Olivia receives a call that they have located the doctor who ran the IVF clinic. The doctor knows that the children created have done all the killings, because he used the clinic as a genetic experiment. He altered their DNA to make a better human being, and the killers are the result.
With the genetic experiments, he tried to reintroduce more primal habits to the human race. The telepathy and desire to protect the "hive" are what drive them to call. He says that there are about 200 such children out there, each one from a different test group.
Back at the hospital, Sean is nervous as he hears the voices starting to panic. Then, a louder voice rings out, the voice of one of the killers who attacked the journalist. That voice tells them all to calm down.
As Lincoln informs Walter this, Walter is more distracted by an alarming sight in Olivia's DNA. She has been dosed with drugs that Walter and William Bell once worked with. They go to Mina Sharpe and demand to see all the remaining samples.
Olivia and Peter are in Boston searching for the doctor's storage facility. Both share their confusion as to what is happening with Olivia's thoughts and feelings. She remarks on the chemicals that caused the explosion in the pilot episode with John Scott. This news alarms Peter because he has never heard of this before. He isn't the cause of what is happening to her mind.
As Olivia and Peter get the storage opened, they are assaulted by several of the modified children. At the same time, two others have come for the doctor. Sean was able to see all this before, but couldn't warn everyone in time. Yet now, he can't hear or feel any of them. It's frightening, but Astrid calms the boy down.
With the case over, Olivia is unsure what to do next with Peter. Her conflicting memories are even more problematic for Peter, who doesn't want to betray his Olivia a second time. Yet he kisses this Olivia, seeing in her the Olivia that he knows and loves. But she leaves him to run into the gas station.
Mina leads Walter and Lincoln to the vault with the drugs, but they are all there. Yet, they are not untouched. Walter is able to drink one since it's just liquid with red food coloring.
When Peter does to follow her, he sees that Olivia is no longer in the gas station. She is waking up to see that she and Mina are tied up in a filthy room far away.