Walter and Peter go to the bridge station and briefly examine the machine. They then meet with the two Fringe teams and Walter explains that Jones is planning to collapse the universes into a gravitational singularity that will destroy both of them. He believes that Jones then plans to create a universe of his own with the laws of physics and nature that he desires. When Broyles wonders how Walter has come to his conclusions, the scientist explains that he dreamed about them, but insists that his subconscious has been working on the problem.
In twenty-seven locations throughout the world, twenty-seven individuals moved to twenty-seven different designated locations and check their timing devices. Each one counts down a particular moment and concentrates, and earthquakes spread out from each of the twenty-seven individuals.
At the bridge station, Peter notes that in the town of Westfield where Jones ran his field test, one small spot in the town survived the annihilation that occurred when the two realities overlapped. They conclude that Jones can create a similar safe zone where he and the people he’s been genetically mutating can ride out the wave of masse destruction. While Peter assures Walter that he did great, everyone else receives calls notifying them of the earthquakes... in both worlds.
The Other Side
Lincoln and Altivia return to Fringe Headquarters and Agent Farnesworth confirms that each of the twenty-seven earthquakes occurred at the same time, and at the same location in both worlds. They suspect that Jones is using amphilicite to generate the convergences and begin searching for him.
At Harvard, Walter examines several pieces of clothing that were found at the epicenter of the Manhattan earthquake. He discovers that the clothing is vibrating at the frequency of the Other Side’s world, not theirs, and Walter tells the team that Jones is trying to synchronize the vibration of the two worlds to merge and destroy them. He warns the others that as the earthquakes continue, the barrier between worlds will inevitably weaken.
The Other Side
Nick Lane, an old high school classmate of the deceased Agent Lee, comes to Fringe Headquarters and talks to Lincoln. Lincoln doesn’t correct his assumption that he’s Lee, and Nick talks about how Lincoln briefly dated his sister Kendra. Nick then explains that he had a vision about being at the center of an earthquake before it happened.
Astrid goes over cell phone footage taken at the Sydney earthquake location and spots one woman who is simply standing there while everyone else panics. Olivia has her try to enhance the image and then receives a call from Lincoln. When he mentions Nick, Olivia recognizes the name as one of her fellow cortexiphan subjects from Jacksonville. She then examines the Sydney image again and recognizes the woman as Sally Clark, another Cortexiphan subject. Olivia suggests that Jones is using the cortexiphan subjects to create the earthquakes and merge the universes.
After reviewing the data, Walter tells the team that Jones is using the cortexiphan subjects to link with their counterparts and change the local vibratory rate, causing the earthquakes. Peter suggests that they shut down the Machine and break the link, and Walter admits that it could theoretically work. However, he warns them that it may be impossible to restart the Machine and if they close it, the healing of the Other Side due to the dimensional breaches would stop. It wouldn’t deteriorate further, but it wouldn’t recover, either. Olivia says that for now they need to focus on finding Jones and stopping his activities, and says that she has an idea.
Lincoln and Altivia bring their alt-Nick to This Side and Walter administers cortexiphan to him in the hopes that Olivia can link with him through the emotional bond that they had as children and tap into his visions. As they work, Altivia admits to Olivia that she likes coming to This Side because they have rainbows, something impossible on the Other Side due to the damage from the dimensional breaches. Walter then hooks Olivia up and she sees what Nick is seeing in his visions. She’s able to direct, Peter, Lincoln, and a FBI team to Salem Bay University where This Side’s Nick is standing in the middle of the quad, preparing to merge with his other self. They capture him but Astrid reports that twenty-six other earthquakes have occurred throughout the world.
The FBI places Nick in custody and Broyles reports that solar flares are beginning to disrupt Earth’s atmosphere. With nothing else to go on, the team starts analyzing the timer device that they took off from Nick, which was built with technology from the Other Side that they hope they can trace. Broyles asks Walter how long they have until the universes merge and Walter admits that he’s surprised it hasn’t already happened. After a moment, Broyles tells them that he’s been called to Washington to discuss the option of turning off the Machine and breaking the link between worlds. Olivia suggests that since she knew Nick as a child, she should try to talk to him.
In the interrogation room, Nick remembers Olivia but refuses to tell her where Jones is. He insists that she doesn’t have to worry about Jones and says that they’re all on the same side. The war that Bell and Walter prepared them for by giving them cortexiphan is here and Nick and the other cortexiphan subjects are working with Jones to destroy the other universe. He hasn’t spoken with any of the others and assumed that Olivia was one of the twenty-six other subjects. When she points out that the earthquakes could kill thousands, Nick says that it’s collateral damage and that after the next offensive, there will be no more earthquakes. Jones will then accept the Other Side’s surrender and they will have triumphed. Olivia tells him that Jones is lying and that Jones wants to destroy both universes, but Nick doesn’t believe her.
As Peter examines the timing device and finds a piece that they may be able to trace, Lincoln comes over to talk to him. Peter asks him what their counterparts think about shutting down the bridge and Lincoln tells him that they’d rather lose the bridge and stop the healing then see their world destroyed. Peter points out that everything will go back to the way it was... except him. However, he admits to Lincoln that he’s happy no matter where he is since he’s realized that home is where the heart is. The timing device activates, revealing that they have six hours until the next and last set of earthquakes.
When she learns they have a deadline, Olivia tries to get through to Nick, telling him that everything he knows and loves will cease to exist. Nick admires her strength but admits that he’s never been as strong. He tells Olivia that after he and his family left Jacksonville, he began to have psychic visions and he prepared to kill himself. However, before he could, he learned that his sister Kendra at killer herself. Jones was the one who explained to Nick that he was a reverse empath, and taught him how to harness and control his psychic energies. Olivia insists that everything Jones has told him about the war is a lie and that their only alternative is to shut down the Machine and stop the Other Side’s recovery.
Nick finally agrees to cooperate and explains that he only met Jones once at a specific location: a warehouse in Manhattan. He guides the team there and Peter and Olivia go inside with a team of agents while Agent Tim watches Nick in the car. However, once they’re alone, Nick summons up his self-hatred and then inflicts his emotions on Tim.
Olivia and Peter check out the warehouse but find no sign of the force field that Jones would need to protect him and his people. When they go out to the car, they discover that Nick has escaped and Tim tried to kill himself. He tells them what happened and they realize that Nick has betrayed them.
With forty-seven minutes remaining, the two teams go to the bridge station. Broyles informs them that Washington will support whatever decision they make. When Walter is unable to come up with an alternative, Broyles has him set the Machine to overload. As they wait for the power to build up, Walter and Secretary Bishop talk and the secretary admits that Peter is the man he would have wished his son to be. Both men realize that if the Machine is shut down, Peter may disappear since he was brought to their reality by the Machine. They discuss Marcus Aurelius, the philosopher-king who worked to the betterment of his people, and hope that they can both do the same.
As the Machine reaches overload, the team says goodbye to their counterparts. Lincoln reminds Peter of what he said earlier about home being where the heart is and tells him that he’s going to the Other Side to be with Altivia. Peter smiles in understanding and wishes him well. Meanwhile, Altivia and Olivia express their admiration for each other, and Olivia tells her counterpart to keep looking for rainbows in her world.
The two teams separate as the Machine reaches overload. Walter shuts it down and the Other Side disappears from the bridge station. Peter is still there and Walter admits that he misses their counterparts more than he can imagine.