Peter comes down and is surprised to find Walter making pancakes. He doesn't seem surprised that Peter is there and tells him to sit down and eat. Olivia comes out and kisses Peter and then hugs Walter, and Peter insists that everything is fine now that he's back with them. Walter tells him that the waffle machine is broken but promises that he'll get the infernal machine fixed, drops it...
... and Peter wakes up from his dream. He goes to the lab and offers Walter pastries, and then suggests that they need the Machine to get him back to his timeline. Peter wants Walter to fix it, but Walter warns that it's powerful enough to destroy universes. When he refuses, Peter insists that he has to get home and Walter is the only person who can help him. Walter hesitates and then describes how he found his wife after she killed herself, and how he was responsible for that and the damage done to the two universes. He points out that it all happened because he tried to help another Peter, insists that he can't help him, and walks away. As he leaves, Peter notices a mirror that Walter is using and gets an idea.
Peter goes to see Olivia at her home. She says that she took a day off because of a migraine and he asks her for a favor. He wants Olivia to get Broyles to give him permission to use the bridge to cross to the Other Side, so he can convince Secretary Bishop to let him use the Machine. When Olivia points out that they can't trust Bishop, Peter says that he doesn't have a choice. She warns that Broyles won't allow it and that there's no way Peter could get to Bishop in any case. Lincoln arrives with chicken soup for Olivia and is surprised to see Peter there. Peter realizes that they can use Lincoln on the other side to get to Bishop. Olivia shows him the papers on Walter's dimension-crossing device, which they've recovered from Lake Reiden, and admits that she was planning on conducting a secret reconnaissance mission. Peter is surprised and notes that she can cross dimensions on her own, and Olivia is surprised to learn that. When he insists that they need the device to get him back, Olivia gives in immediately and says that they'll get the device from Massive Dynamic.
On the Other Side at Battery Park Bus Terminal, a boy goes into the restroom while his mother waits outside. As he enters the restroom, he hears two men fighting in the stall. He goes out to get his mom, who reports the incident to a transit officer. The officer goes in and opens the cell, and finds a man with transparent skin standing over a dead man. The transparent shapeshifter runs out into traffic but is hit by a bus.
Brandon comes to see Secretary Bishop with the shapeshifting technology and tells him that they've pinpointed a signal that should lead them to the person responsible for the new shapeshifter prototypes. Bishop tells him to leave the tech and dismisses him.
At the bus terminal, Bolivia and Agent Lee investigate the scene. Sgt. Elias Kane arrives with the military and orders everyone out, including Bolivia and Agent Lee. They confirm that Bishop gave the orders and Agent Lee is ready to leave, but Bolivia isn't convinced.
On This Side, Lincoln calls Olivia and Peter as they drive through Connecticut on their way to the Orpheum Theater. He tells them that he has the device and will meet them there, and Peter assures her that the Orpheum is a weak spot between universes. At the theater, Olivia has another headache but insists on remaining there to help them return. Lincoln arrives, without his glasses and dressed like his Other Side counterpart, and he and Peter prepare to go through. Peter thanks Olivier for her help and goes through, and Lincoln steps through after him. They find themselves in the Orpheum on the Other Side.
At Fringe Division, Agent Farnsworth picks up a dimensional breach and alerts Captain Broyles. He has her send Bolivia and Agent Lee there.
Lincoln and Peter exit the Orpheum and leave.
At the DoD headquarters on the Other Side, Kane arrives with the shapeshifter's victim and brings it to the lab. Bishop orders Brandon out and then cuts open the corpse and removes its memory disk.
Peter and Lincoln approach the DoD's dock to Liberty Island, and Lincoln claims that Peter is his prisoner. He tells the MP, Corporal Wheeler, that it's a covert delivery and the MP eventually agrees to let them through. However, he asks for Lincoln's show-me. When Lincoln says he lost it, the guard asks for his handprint. Lincoln has no choice but to agree and his handprint passes the security check. As they go to the ferry, Peter admits that he's impressed with Lincoln's knack for deception.
Bolivia and Agent Lee go to the Orpheum but don't find any signs of degradation. They figure that it's a false alarm but Broyles isn't convinced. He recalls them back to headquarters, while Bolivia considers the dead man at the bus terminal. She figures that he's a shapeshifter who caught in mid-transformation and is connected to the new shapeshifters that those on This Side are accusing them of sending. Bolivia figures that Bishop had the corpse removed by the military to cover up his own involvement. They get in the car and Agent Lee discovers that his show-me doesn't work because it was reported lost. They confirm who reported it lost and Agent Lee Wheeler. Wheeler looks over at Lincoln and Peter, who are still waiting for the ferry.
Peter tells Lincoln to go back to the Orpheum and go through, but Lincoln refuses to go and insists that he go through. Bolivia and her team arrive and arrest them both, and Peter insists that he needs to talk to Bishop. Bolivia demands to know who he is.
Broyles calls Bishop and tells him about the intruders, and that one of them claims to be his son Peter Bishop. Shocked, Bishop tells him not to tell the This Side Fringe anything until they've learned more.
As Lincoln and Peter are taken to Fringe HQ, Peter realizes that Lincoln was acting on Olivia's orders. Lincoln insists that they're fighting for their people and they needed the information to stop the shapeshifters. Peter tells him that it's not his fight. Meanwhile, the driver, Agent Murphy, gets a phone call, accepts new orders, and drives away from the convoy. Bolivia calls Murphy but he refuse to answer. When Murphy's partner Cole asks what's going on, Murphy shoots him dead.
Murphy pulls over in an alleyway and orders his captives out. He tells them to remove their cuffs and prepares to shoot them, saying that he has his orders. The dying Cole manages to shoot him, and Peter struggles for the gun and finally manages to kill him. Peter frees Lincoln and tells him that they're doing things his way now.
Farnsworth directs Bolivia and Lincoln to the alleyway, and then reports that the transport is on the move even though there are agent transponders in the alley. Lincoln drops off Bolivia and follows the transport into an alleyway, and then cuts them off. Lincoln gets out but Agent Lee realizes that Peter has escaped. They realize that Lincoln created the distraction to let Peter escape, and Agent Lee asks why he killed two Fringe agents. Lincoln points out how unlikely that is but Agent Lee doesn't believe their story that someone ordered Murphy to kill them. When Bolivia wonders who would want them dead, Lincoln tells them that Bishop is the one responsible. He explains that This Side has been infiltrated by shapeshifters and Bishop must have people inside the Other Side's Fringe Division. Lincoln suggests that they trace the call on Murphy's phone. When they wonder why he's trusting them, Lincoln tells them that Peter said he could trust Bolivia because she's a good person. Bolivia says that they'll sort it out at headquarters and leaves with the prisoner.
In Tarrytown, NY, Elizabeth Bishop arrives home and realizes that someone is in the house. She triggers the silent alarm and heads for the door, but Peter steps out. He asks to speak with her husband, and Elizabeth realizes that it's her son. She sits down with Peter and explains that she's learned to accept a great deal thanks to Bishop, and recognized Peter by his eyes. Peter explains that he's not the Peter from either side, but he needs to get back to his own place. Elizabeth admits that she managed to deal with the tragedy of her son's death by knowing that in some other universe, there was a Peter who survived and fell in love and had a life. She believes that Bishop would do whatever he could to help Peter and prepares to call her husband, but Peter warns that people working for Bishop tried to kill him. Elizabeth insists that Bishop needs to know about it, but Peter figures that he already does.
Soldiers arrive in response to the alarm and Elizabeth asks for Peter's gun. He reluctantly hands it over and she assures Peter that she won't let anything happen to him this time. Elizabeth lets the soldiers in but orders them to transport her and Peter to the DoD to see Secretary Bishop. The head soldier agrees but restrains Peter.
At Fringe Division, Bolivia and Agent Lee handcuff Lincoln in a maintenance closet and admit that Murphy's phone logs confirmed that he received a call. They're going to trace the call and Lincoln will have to wait until they're done. As they leave, Agent Lee warns Bolivia that they're breaking orders and hopes she knows what she's doing.
The soldiers take Elizabeth and Peter to Bishop's office. She insists that it's a miracle that their son has been brought back to them and Bishop agrees. He tells Peter that he's dreamed of standing with Peter for so many years and tells the soldiers to remove the restraints and leave them. Peter tells Bishop that he's not his son, and Bishop is well aware that he isn't. He asks Elizabeth to leave them alone to talk for a few minutes. Once she goes, Peter congratulates Bishop on his performance pretending that he was surprised. Bishop explains that he's been monitoring feeds from This Side, and Peter tells him that he knows he tried to have him killed. He doesn't know why but figures that Bishop sees him as a threat. However, he tells Bishop that he doesn't care about the struggle between the two universes. All he wants is access to the Machine so he can go home. Bishop notes that his decision must have been difficult if Peter knows the terrible things he's done, and Peter admits that he didn't have a choice.
Brandon comes in and Bishop says that Peter has accused him of being responsible for the prototype shapeshifters. He tells Brandon to confirm if Peter's suspicions are true, and Brandon says that Bishop couldn't have been responsible. Bishop then shocks Brandon with a device. The scientist falls to the floor, his skin turning transparent, and Bishop tells Peter that everything is not what it seems.
Bishop has Brandon taken to the lab and restrained, and tells Peter that he's suspected Brandon for weeks and had him followed. He also is aware that elements of their government have been infiltrated, but couldn't sound a general alarm without causing a widespread panic. Peter tells him that he has to expose the shapeshifters, but Bishop admits that the device he used on Brandon would have killed a normal human being. He then admits that he can only trust Peter because he has no alliances to either side. Bishop asks Peter to tell This Side that he's not their enemy in return for doing everything in his power to help Peter get home. Peter hesitates and then admits that he was wrong about Bishop and that he's not the man he thought he was. In response, Bishop says that Peter is exactly the man he thought he would be.
Bolivia has Farnsworth confirm that the call came from the abandoned Flatiron District and wants Agent Lee to help her check it out. He's reluctant to do it so but Bolivia wonders what it means if Lincoln is right. They finally go to Broyles, who knows that they ran a trace on Murphy's phone. Bolivia asks for permission to investigate and Broyles agrees. Once they leave his office, Broyles tells his superior that they're on their way to the man... David Robert Jones. Jones is in a warehouse with tubes filled with shapeshifters in suspension tanks.
On This Side, Olivia wakes up at the Orpheum and finds the Observer looking at her. She asks what he wants and he echoes her words a second later. The Observer then addresses her by name but starts gasping for breath. Olivia realizes that he's been shot, but the Observer continues and tells her that in every possible future that he has seen, Olivia has to die. Olivia turns to get her coat and he vanishes in the second it takes for her to turn around.