Walter analyzes the body of a shapeshifter and then reconnects with an old patient that has the ability to distinguish the people from the other world. Olivia finally recalls her encounter with Belly.

Olivia and Peter look into some patients of mental institutions that regain their mental state after having gone through a brain intervention performed by a shape-shifter named Newton. This is directly related to Walter and his brain.

An earthquake from the other side is being felt on our Universe as well. Furthermore, the only survivor seems to be from the alternate Universe. Walter attempts to get Olivia to "recover" her ability to make out things from the other side.

The Fringe team investigate a train full of people who died in a mysterious way. Olivia and the others then meet the astrophysicist who was responsible for the "experiment" and who can reset the time.

The body of a male teenager is found along with shapeshifter marks. Walter examines the embryo of a shapeshifter, that came from the alternate Universe. The team try to anticipate the shapeshifters' next moves.

Peter stumbles across Newton and his people while running away from Walter and the FBI. He teams up with the local sheriff to try and find Newton.

Three men abduct and keep a family tied up and gagged in the living room. Two of them dig the basement while the third one watches the family. The men find a box and decide to take a peek inside. The two men and the family immediately die. The Fringe Division investigate the case and Walter performs an autopsy on the bodies. Soon he finds that they die because they have been exposed to an ultrasound signal. Walter receives an envelope from William Bell's lawyer as inheritance and he discloses to Astrid what William left for him. Meanwhile the alternate Olivia and Newton, who had hired the men to find the box and bring to him, plot a scheme to retrieve the box. Then they set in motion a Machiavellian plan.

When the American Senator James Van Horn has a serious car accident, he immediately goes to surgery; however Newton invades the hospital and abducts him shooting the staff. There is a shootout with Broyles and Newton shoots Van Horn in the eye. The Fringe Division finds that the senator is a shapeshifter and they take his body to Walter's laboratory. He finds that it is possible to revive the shapeshifter and recover his data disc. But the alternate Olivia calls Newton and he sends the shapeshifter Ray to the hospital to retrieve the disc. When he returns home, Newton orders him to kill his family. However Ray is connected to his wife and son and refuses to follow the order. What will happen?