Walter and Olivia discover that Peter has agreed to go back with his real father, the Walternate, back to his own dimension. An Observer leaves them a paper indicating Peter to be the major subject of a prophecy, which foretell him being the one responsible for the end of the world. In order to warn Peter of his impending role, the Fringe Division work with Massive Dynamic to come up with a way to cross over. They come up with a plan to use Olivia's dimension-hopping ability by amplifying herself with three other Cortexiphan subjects who have activated their abilities (from previous episodes): Nick Lane, Sally Clark and James Heath. The team comprising of Walter, Olivia, Nick, Sally and Heath successfully head over the Other Side, but Heath dies shortly after arrival, while the rest manage to escape the alternate Fringe Division when they used their technology to sense their arrival. It is revealed that Walternate is the Secretary of Defense on the Other Side. While Walter's team head to meet William Bell at Central Park, Peter reunites with his real mother. Walter's team is split up when they believe that Bell has betrayed their location and the alternate Fringe Division attacks them. Nick and Sally are killed, but not before seriously burning the Fringe principal investigator, Lincoln Lee. Walter is shot and ends up in hospital. Olivia follows her alternate counterpart and encounters Bell, who insists he never betrayed them, and tells her that Walter is in trouble. Walternate is seen leaving with the final component of the device Peter will be a part of.
Walternate is informed of the original Walter's presence in hospital, but William Bell and Olivia manage to rescue him first. Walternate lies to Peter about the machine's real purpose, claiming that it can help heal the other world. Alter-Olivia and Alter-Charlie are unable to capture Walter, but Alter-Olivia sees a surveillance shot of Olivia and Walter and goes to confront Walternate. Peter meets Alter-Olivia who drives him to his new apartment. Walter and Bell go to Harvard to collect equipment needed to return home and Walter reveals his intense dislike for him, considering him a selfish war profiteer while he was locked away for 17 years and is still broken inside. Bell reveals the alternate universe equivalent of himself died in a car accident as a young man. Olivia confronts Alter-Olivia who recognizes that Olivia has feelings for Peter. After a fight Olivia knocks Alter-Olivia unconscious and poses as her. Peter discovers the machine is symbiotic and needs a particular human to control it: him. Olivia and an oblivious Alter-Charlie go to collect Peter to move him for his own safety. Olivia knocks out Alter-Charlie and reveals herself to Peter, as well as filling him in on the machine's real purpose and Walternate's intentions. Peter states he doesn't belong in the other world or Olivia's world. Olivia reveals her feelings for Peter, making him decide to leave with her. They race to meet up with Walter and Bell at the Opera House, but Alter-Olivia and a team of Fringe Commandos catch up with them there. Bell and Olivia hold off the assault while Peter and Walter set up the dimensional device to return home. Without a fuel source to power the device, Bell sacrifices himself to create a nuclear reaction using his body's unstable molecular state. Before dying he reveals that he took Walter's memories away at his own request, referring to what Walter was becoming. Walter tells Bell that he was wrong about him and forgives him. Olivia, Walter, and Peter return home successfully. Peter tells Walter he'll never understand him, but Walter travelled into another universe twice to save him, which counts for something, so Peter forgives him. Olivia goes to the typewriter communication station to await orders and is revealed to be Alter-Olivia infiltrating our side. The Olivia from our world is seen in a military detention center on the other side. Walternate visits her, cruelly stares at her without speaking then leaves her in the dark isolation of solitary confinement.
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