The Fringe Division visits the Massive Dynamic to see the Doomsday Machine and the presence of Peter assembles the device. He is submitted to tests by Dr. James Falcon against Walter's will. Walter asks Nina to find William Bell's research since he wants to restore his brain to increase his IQ and help Peter. Meanwhile Broyles gives access to the main frame where the alternate Olivia's files are to help the investigation and they suspect there is a mole accessing the information. Soon they find that someone is killing the shapeshifters. Who might be the killer?
When a scientist is killed by a blue dust that grinds his bones up, the Fringe Division investigates the case and suspects a biological attack. The investigation leads them to a former marine that flees but is hit by a car. In coma, Walter recalls his Cortexiphan patient Simon Phillips that is capable to read mind. Olivia, Peter and Walter try to convince Simon, who leaves in a desert area, to help them to locate the terrorists, but he is sensitive to other people since he cannot control his ability. Simon agrees to help and also disclose Peter's real feelings for her.
In the parallel universe, the Fringe Division investigates a case where a man was eaten from inside out by an extinct beetle. Meanwhile Broyles is considered missing and Lincoln is the head of the division. Olivia welcomes her boyfriend Frank that has just returned from Texas and wants to propose her. When a second man is also eaten by the insects, the Fringe Division identifies the scientist Dr. Armand Silva that was researching the cure for avian flu using this insect. Lincoln and Olivia goes to his address and split. Lincoln is locked in a refrigerating chamber ...
The Fringe team attempts to find out what process enables people to become lighter than air and float. Peter and Olivia deal with trust issues in their relationship, while Walter becomes increasingly obsessed with retrieving William Bell's consciousness from beyond the grave.
As the Fringe team hopes to alleviate Olivia's possession quickly, Agent Lincoln Lee of the F.B.I. meets them for the first time over the curious case of what he calls "the compassionate soul vampire."
In the parallel universe, Olivia is submitted to an EPV test since her sister died during the delivery of her baby. When she returns to her apartment, she is abducted and taken to a facility where she is submitted to a procedure that accelerates her pregnancy. Meanwhile the Fringe Division seeks her out while her mother Marilyn is informed that Olivia's EPV was confirmed.
Peter successfully enters the machine with Olivia's help, and is transported to the future days where Walternate's universe is the one which has been destroyed. Walter learns about the origins of the machine and its ultimate purpose and sends back Peter to change his choice but gets lost in time warp.
Peter creates a bridge between the two universes to force both sides to work together in resolving the problems in both universes and then he vanishes and is forgotten as if he had never existed. Meanwhile Agent Lincoln Lee and his partner Robert chase a criminal. Lincoln kills the criminal but a second one with a translucent skin kills Robert. Olivia assumes the case but Lincoln notes her plate and follows her. Soon they team-up to chase the mysterious criminal that is killed by Olivia. Walter finds a device in the man and Olivia gives to her alternate version that ...
Two bullying boys die and exhibit an alarming state of rapid decay. Their would-be victim, an extremely lonely boy, has a remarkably unusual connection to the killer. Meanwhile, Walter fears for his sanity.
Olivia is haunted by an energy force that attracts metallic objects and Walter recalls his subject 9 that has the ability for astral projection. They chase the patient Cameron Jones but they conclude he is not the responsible for the energy force. However and Cameron faces the force, something happen.