The First Wave breaks into a mental hospital and cures a long-term patient suffering from schizophrenia. When the Fringe team investigates, Olivia discovers that the group's leader has one of the heads stolen from cryogenic storage months earlier. Meanwhile, two other mental patients are cured of their schizophrenia and the team soon realize that something was taken from each patients' brain... and Walter holds the key to realizing what First Wave is after.

When the Fringe Team visits Massive Dynamic’s assembly of the doomsday device, Walter becomes greatly concerned for Peter’s well-being, so he turns to Nina for added brain power to understand the relationship between Peter and the superweapon. Meanwhile, the discovery of a dead body triggers an intense investigation.

The beginning of the end is triggered when Walternate finds a way to wreak havoc “over here."

In an effort to find a way home, Peter journeys to the Other Side to confront Walternate. However, his venture proves more dangerous than expected. Meanwhile, Olivia receives a dire premonition from an Observer.

Walter travels to the Alternate Universe to assist in the investigation of a Fringe event with ties to both worlds. Meanwhile, David Robert Jones reveals his next target.

The Fringe team - preserved in amber for 20 years - is now a rebel resistance team fighting for freedom. Peter, reunited with his now adult daughter, Etta, sets out to find out what happened to his wife and Etta's mom - Olivia - as they start their mission to save the world from the Observers.

The Fringe team revisits the Harvard lab, now under Observer control, to try to find the information they need as the team fights on in their mission to save the world.