Peter is dreaming that thing are back to normal and that he is having breakfast with Walter and Olivia at home. Walter tells his son that the waffle machine is broken and he’s making pancakes, and promises to get the infernal machine working as soon as he can. He then drops the machine as Peter stares in horror... and then wakes up.
Walter is working at the lab when Peter comes in and tries to convince him to use the Machine to send Peter back to his own timeline. Walter refuses, pointing out that the Machine is powerful enough to destroy universes. When Peter persists, Walter talks about how Elizabeth committed suicide after the death of their Peter, and how her death and the death of countless others on two worlds were his responsibility because he tried to help another Peter. As he walks away, Peter notices a mirror in the lab and gets an idea.
Peter goes to see Olivia at her apartment, where she has taken a day off because of a migraine. He asks her to go to Broyles and get permission for him to use the bridge to cross to the Other Side and convince Walternate to let him use the Machine to return to his timeline. Olivia insists that they can’t trust Walternate, who they suspect sent the new shapeshfiters after them, and that Walternate would have Peter arrested in any case. Lincoln arrives with chicken soup for Olivia and Peter realizes that they can use him to get to Walternate since Lincoln looks just like Agent Lee, the lead agent on the Other Side. Olivia admits that she has the Massive Dynamic requisition form for the dimension-shifting device that their Walter used at Lake Reiden, which they recovered afterward. She had planned to use it to sneak over to the Other Side herself and find out about Walternate’s involvement with the new shapeshifters. Peter wonders why she needed the device, and Olivia is surprised when he says she can shift dimensions on her own. He says that he needs the device to get home and it has to be their priority, Olivia agrees and says that they can get the device out of storage and use it.
The Other Side
A mother and son are at the Battery Park Bus Terminal and she sends her son into the restroom. He hears two men struggling in a stall and goes outside to tell his mother. She calls a transit cop over to investigate and he discovers a transparent-skinned shapeshifter standing over a dead man. The shapeshifter runs out and into the street, leaping over a bus, but is hit by another bus and killed.
Brandon Fayette comes to see Walternate and explains that they’ve examined the memory disk from the transparent shapeshifters and pinpointed a signal. Walter tells him to leave the tracking device with him and Brandon leaves.
At the bus terminal, Dunham and Agent arrive to examine the shapeshifter, but a military detachment comes in and secures the scene, ordering the Fringe agents out along with everyone else. The agents confirm that Walternate was the one who gave the commander, Sgt. Elias Kane, his orders. Lee is ready to lee but Dunham isn’t convinced that everything is on the up and up.
Peter and Olivia drive to the Orpheum Theater, the place where Peter crossed over before in his timeline. Lincoln meets them there with the transition device, while Olivia complains about a migraine. However, she insists on staying at the Orpheum and waiting until they come back. Lincoln, dressed like his counterpart, is ready to go. As they prepare to transition, Peter thanks for his help and then the two men go to the Other Side.
The Other Side
Agent Farnsworth picks up a dimensional breach and warns Captain Broyles, who orders Dunham and Lee to check it out.
At DoD Headquarters, Kane delivers the shapeshifter’s body to Walternate and Brandon. Walter orders Brandon and his staff out and then cuts into the corpse and removes its memory disk.
Lincoln takes Peter to the DoD’s ferry dock and tells the MP, Corporal Wheeler, that Peter is his prisoner. The MP asks for his show me and Lincoln claims that he lost it. Lincoln passes the handprint scanner but the MP reports the show me as missing. As they go to the dock, Peter admits that he’s impressed with Lincoln’s knack for deception.
At the Orpheum, Dunham and Lee find no sign of degradation and Farnsworth confirms that the breach has disappeared. Broyles recalls his agents to headquarters and as they go back, Dunham wonder about the dead man. From the brief glimpse that they got, she concludes that it was one of the new shapeshifters that the This Side Fringe Division has accused them of sending. Dunham figures that Walternate is involved and had the soldiers remove the body to cover up any evidence of his involvement. When Lee tries to start his car, he discovers that it won’t work because his show me has been reported missing. He calls Wheeler, the man who reported it, and Wheeler tells Lee that “Lee” is waiting for the ferry with a prisoner.
As they wait for the ferry, Peter tells Lincoln to go back to This Side. However, Lincoln insists on going, saying that he needs to find Walternate’s secure room and any evidence linking the Other Side to the shapeshifters. Before they can argue it out, Lee and Dunham arrive with their team and arrest both men. Peter insists that he needs to talk to Walternate but Dunham want to know who he is.
Broyles calls to tell Walternate about the intruders, including the fact that one of them says his name is Peter Bishop. Shocked, Walternate tells him to secure the prisoners but keep their This Side counterparts in the dark.
Agents Murphy and Cole drive Peter and Lincoln in a transport while Dunham and Lee follow. Peter and Lincoln argue about how Lincoln was following Olivia’s orders to break into Walternate’s office. Lincoln defends his actions, saying that they need the information to stop the shapeshifters, but Peter insists that it’s not his fight. Murphy gets a phone call with orders and then drives in a different direction. Dunham tries to call Murphy but he ignore her. When Cole tries to stop Murphy, Murphy shoots him. He then pulls into an alleyway, orders Peter and Lincoln out, and prepares to shoot them while “trying to escape.” The wounded Cole manages to shoot Murphy and Peter jumps the agent. They struggle and Murphy is shot, and Peter frees Lincoln and tells him that they’re doing things his way now.
Farnsworth tracks the transport and sends Dunham and Lee there, but then confirms that the transport is moving again. Lee drops Dunham off and she discovers the two dead agents. Meanwhile, Lee and his team cut off the transport only to discover that Lincoln is the only one in it. They realize that Lincoln is the distraction and Peter has gotten off elsewhere. Lincoln tries to convince them that he and Peter didn’t kill Cole and Murphy, but Lee is skeptical. He warns them that Walternate is responsible and suggests that they trace the last call that Murphy received. When they wonder why Lincoln trusts them, he tells Dunham that Peter said that she was a good person at heart and he could trust her. Dunham tells Lincoln that they’ll sort it out at headquarters and takes him in.
Elizabeth Bishop returns to her home in Tarrytown, NY and realizes someone is in the house. She triggers the silent alarm and tries to escape, but Peter emerges from hiding. He asks to speak to Walternate and Elizabeth immediately realizes that Peter is her adult son. They talk and Peter tries to explain that he’s not her Peter, and that he needs her help to get back to his own timeline. Elizabeth admits that she managed to get through her grief by accepting that somewhere in the multiverse, a version of her son survived, fell in love, and had a life. She believes that Walternate will help Peter and prepares to call him, but the MPs arrive in response to the silent alarm. Elizabeth asks for Peter’s gun, warning that they’ll kill him otherwise. He reluctantly surrenders it and Elizabeth convinces the MPs to take them both to her husband.
At Fringe Division, Dunham and Lee lock Lincoln in a closet and tell him to wait while they trace the call to Murphy’s cell phone. As they go, Lee warns Dunham that she’d better know what she’s doing since they’re breaking orders.
The soldiers take Elizabeth and Peter to Walternate’s office at the DoD. Walternate appears surprised to see Peter and admit that he’s dreamed of being reunited with Peter for years. He then orders the MPs out and admits that he knows that Peter isn’t his son. Walternate then asks Elizabeth to leave. Once she’s gone, Peter congratulates Walternate on his performance, figuring that he knew all along who he was. Walternate admits that he knew because he was secretly monitoring This Side communications, and Peter accuses him of the attempts on his life. He insists that he’s no threat and doesn’t care about either of the two universes. Walternate figures that Peter had to face a terrible decision knowing the terrible things that he’s done, and Peter admits that he has no choice.
Brandon comes in and Walternate asks him to confirm that he had nothing to do with the creation of the new shapeshifters. Brandon tells Peter that Bishop wasn’t responsible, and Walternate then zaps him with an electronic device. When Brandon falls to the floor, his skin turns transparent, and Walternate tells Peter that everything isn’t what it seems.
In a secret lab, Walternate has the Brandon shapeshifter secured and explains to Peter that he suspected Brandon for sometime. He also believes that the shapeshifters have infiltrated various levels of the Other Side’s government, but can’t go public for fear of setting off mass panic. When Peter suggests that he used the device on the shapeshifters to prove who they really are, Walternate warns that the charge will kill a normal human. He asks Peter to tell This Side that he has nothing to do with the new shapeshifters, and trusts Peter to do so because he has no stake in the outcome for either side. Realizing what Walternate has had to face, Peter admit that Walternate isn’t the man that he thought. In response, Walternate tells him that he is exactly the man he thought he would be.
Dunham has Farnsworth trace the call to the abandoned Flatiron District. Lee is reluctant to do so without Broyles’ approval, and they go the captain. He knows they ran the trace and gives them permission to investigate. Once they’re gone, Broyles calls his secret master: David Robert Jones. The captain warns Jones that they’re on their way. Once Jones hangs up, he looks around the warehouse where he’s established a lab filled with chambers holding shapeshifter prototypes.
At the Orpheum, Olivia wakes up and discovers a stranger watching her: the Observer, September. He initially repeats her words back to her as soon as she says them, and she realizes that he’s been shot. The Observer calls her by name and tells her that in every possible future that she’s seen, Olivia has to die. Olivia insists on getting him to the hospital and turns to get her coat, and the Observer disappears.