Walter and Peter come to see the Machine and Peter assures Walter that he looks great. They then meet with the teams on both sides and Walter tells them that Jones is planning to collapse the universes in order to create a gravitational singularity. The energy will then expand again, creating a big bang of mutual destruction. The others wonder why and Walter explains that Jones plans to create a universe in which he designs the laws of physics and nature. When Broyles wonders how Walter deduced all this, Walter says that he had a dream. The others are skeptical, but Secretary Bishop says that he's learned that anything is possible and stands by his counterpart's theory.
In Sydney, Australia, a woman at the harbor checks he watch for a precise time and goes to a precise place.
People in Beijing, the Himalayas, Manhattan, and twenty-three other locations follow similar instructions and synchronize their actions.
At the precise time, all twenty-seven people take designate positions and concentrate, and the ground around them starts to shatter.
At the bridge, Peter points out that at Westfield, one small area survived. They figure that Jones can create a safe zone and then will populate his new universe with the genetic mutations that he's been creating. A soldier summons Secretary Bishop away and everyone else receives calls. While they talk, Peter assures Walter that he did great and that everyone listened to him. The reports come in of earthquakes on both worlds and Walter warns them that it's Jones.
On the Other Side at Fringe Headquarters, Agent Farnesworth determines that the earthquakes all started at the same time, and in the same places in both universes. They figure that Jones is using amphilicite and start searching.
At Harvard on This Side, Walter is going through a box of old clothing. He tells them that the clothing was recovered from the epicenter of the earthquake in Manhattan. The clothing is vibrating on the pattern of the Other Side and Walter explains that Jones is trying to get the two universes to vibrate at the same frequency. He warns that they will see many more earthquakes because the vibrations are weakening the barriers between the two universes.
Nick Lane comes to see Lincoln at Fringe HQ and reminds him that they grew up in Philadelphia together, and Lincoln went out with his sister Kendra. Nick explains that he had a vision that he was at the center of an earthquake even though he didn't know about them yet.
Astrid goes over footage of the earthquake in Sydney and spots the one woman who is just standing at the epicenter. Olivia has Astrid try to get a clearer image and then gets a call from Lincoln. He explains about Nick and figures that he saw the earthquake on This Side. Olivia recognizes Nick's name and hangs up, and then looks at the image again and confirms that it's Sally Clark. She explains that she, Sally, and Nick were in the cortexiphan trials again and figures that the cortexiphan subjects are being used by Jones as triggers.
Walter works it out and explains that Jones is using the cortexiphan subjects' abilities to link with versions of themselves in the alternate universe and change the local vibratory rate. When the two universes merge in those spots, the earthquakes occur and the universes start to collapse. Peter wonders if the connection between the two universes is facilitating the psychic links and suggests that they sever it by turning off the Machine and closing the bridge. Walter admits that it could theoretically work, but warns that they may not be able to start it again. If they close it, the healing of the Other Side would stop and it would get neither better nor worse. Olivia says that their best option is still to find Jones and stop the attack, and says that she has an idea.
Bolivia and Lincoln take Nick to the bridge and bring him to This Side. Walter then administers cortexiphan and Olivia explains that since she and her Nick shared an emotional bond so she's hoping they can find the Nick on This Side by using the Other Nick as a point of contact. As they work, Bolivia explains that she likes coming to This Side and enjoying the rain and the subsequent rainbows, since the weather on the Other Side has been altered by the dimensional breaches.
They hook up Olivia to Nick and she manages to tap into his visions. She sees This Side's Nick and pinpoints his current location in Salem, Massachusetts. Peter and Lincoln take a team there while Olivia places him at Salem Bay University. She realizes that he's going to trigger another earthquake and realizes that he's in the quad. Peter and the others arrive there and capture him, and Olivia stops out of her trance. However, Astrid reports that other earthquakes are occurring throughout the world.
This Side's Nick is placed in custody while Broyles tells the team that solar flares are on the rise and causing disruptions in Earth's magnetic field. He wonders how Jones convinced twenty-seven cortexiphan children to destroy the world. The watch that Nick was using is made from parts on the Other Side and they hope they can trace the parts there. Broyles then asks how many quakes will it take to collapse the universes, and Walter admits that he's surprised that it hasn't happened already. At that, Broyles says that he's been called to Washington to discuss turning off the Machine and wonders if it's the best option. Olivia volunteers to talk to Nick since they knew each other as children.
Olivia enters the interrogation room and he immediately remembers her. She asks him where Jones is and he refuses, explaining that she doesn't have to worry about him. When Olivia asks why, Nick tells her that she's on the same side as the rest of the cortexiphan children, and that the war they were prepared for is beginning. He insists that Jones is on their side and protecting them. Walter, watching through the one-way mirror, realizes what is going on. Meanwhile, Nick says that he doesn't have contact with the others and figured that Olivia was working with them. He explains that the earthquakes are collateral damage in the war and are almost over. Jones plans to launch one more offensive and then claims the Other Side will surrender. Olivia explains that the two universes are allies now and Jones wants to destroy them both. She asks again where Jones is but Nick doesn't answer.
Peter examines the timing device while Lincoln looks on. He finds a labeled resistor and figures that it's traceable, and then asks Lincoln what the Other Side's take on closing the bridge is. Lincoln says that they want to survive and realized that they don't have a choice, and Peter figures that at least everything will go back to the way it's supposed to be... with the exception of himself. However, he assures Lincoln that home is where the heart is and he'll be happy no matter where he is. The timer activates on its own, indicating six hours until the next earthquakes.
Olivia tells Nick about the coming earthquakes and warns him that everything he knows and loves will cease to exist. Nick gazes at her and points out that she's always the strong one, but he's never been strong. He tells Olivia that when his family moved away from Jacksonville, he started having psychic episodes and they got to the point where he tried to kill himself. His sister, Kendra, killed herself on the night that Nick was considering killing himself. Jones told Nick that he was a reverse empath and his emotions were contagious, and taught him how to control and channel the energy in his brain so he could protect This Side. Olivia sympathizes with Nick but tells him that everything Jones has told him is a lie. She explains that they still have a way to stop Jones but it will stop the healing of the Other Side.
Nick agrees to cooperate and they show him the information that they have on Jones. Walter figures that Jones will need a powerful force field, and Nick says that Jones always came to him. However, one time they met at a warehouse filled with equipment and Nick offers to take them there. Peter and Olivia lead a team there and they break into the warehouse while Nick waits outside in the car. He worries that they've taken too long and figures that something has gone wrong. Nick complains to the agent guarding him about how pathetic he feels and says that he should've killed himself, and then imposes his emotions on the agent.
Inside the warehouse, the team discovers that there's nothing there but an air conditioning unit. Agent Tim calls them to say that he got sad and tried to kill himself. Nick is gone and they realize that he set them up.
With forty-seven minutes remaining, the two teams wait at the bridge. Broyles informs them that Washington has decided to support whatever the two teams decide. Walter admits that he hasn't been able to come up with an alternative and they prepare to shut down the Machine. Peter activates the device and they initiate an overload. While Peter notifies the others, Walter tells his counterpart about the interface they're using. Secretary Bishop notes that Peter is a remarkable man and the man that he would have wished him to be. Walter walks off into a corridor and sits down, and Secretary Bishop sits down with him. They have both realized that if they shut down the Machine then Peter may disappear since it was the Machine that brought him there. Walter admits that he's come to accept that Peter isn't his, and Secretary Bishop hopes that no matter what happens, the two of them will be able to continue working for the betterment of their people.
As the Machine approaches overload, the team says goodbye to their counterparts. Lincoln reminds Peter of what he said earlier and informs him that he's going to go with Bolivia to the Other Side. Peter offers his hand and wishes him well. Meanwhile, Bolivia tells Olivia that there are a lot of things that she admires about her, and Olivia says that she feels the same. Olivia tells her counterpart to keep looking up for rainbows and walks away, and Lincoln joins Bolivia, Agent Farnesworth, and Secretary Bishop. The system overloads and Walter shuts down the Machine. Everything flickers and the Other Side part of the bridge fades away. Peter is still there and Walter admits that he'll miss their counterparts more than he imagined.