In the conference room at the Bridge, Walter tells Peter, Walternate, and the Fringe teams that he believes David Robert Jones is trying to collapse both universes. His goal is to create his own universe, in which he controls the laws of physics and nature.
When Walter says he came to this conclusion after having a dream, everyone becomes skeptical. Walternate reminds them that anything is possible.
Meanwhile, in Sydney, Australia, a woman stands at a precise point and watches her alt-universe watch count down from 1:20. Simultaneously, others do the same in Beijing, Nepal, and Manhattan. All remain completely still while the ground starts shaking.
In the meeting, Peter recalls how, after Jones destroyed both towns of Westfield, one area stayed standing. Maybe that was a test. Walter theorizes that he's built a safe zone for himself and his new species. They're interrupted by news of earthquakes all over the world - both worlds. It's Jones.
Agent Farnsworth reports 27 quakes, registering between 5.7 and 7.1 on the Richter scale, all starting at the same time.
At Harvard, Walter shows Peter, Olivia, and Astrid that items from the Manhattan epicenter are vibrating in the key of E - a different frequency than either universe. (This Side is C, the Other Side is G.) Jones aims to make the two universes vibrate at a common frequency, creating the earthquakes and weakening the barrier between them. If he does it enough times, in the right locations, collapse is inevitable.
On the Other Side, Lincoln meets with Nick Lane, who thinks that Lincoln is his deceased doppelganger, a childhood friend. Nick had a vision of standing in the middle of the earthquake - before he knew it had happened. Lincoln phones Olivia, who's viewing footage of the Sydney woman standing still amid the chaos. Lincoln says the guy described a Manhattan without Twin Towers, so he somehow saw the quake on Olivia's side.
When Olivia hears Nick's name, she realizes the Sydney woman is Sally Clark. They're former Cortexiphan kids. Jones is having them psychically link to their doppelgangers. By drawing on their alternates' frequency, they change the vibratory nature of the area around them, effectively merging the universes.
Peter suggests closing the Bridge. Turning off the Machine could break the link. Walter argues that they may never get the Machine started again, separating the two sides forever. The Other Side's healing would end, but things wouldn't get worse. But first, they'll try to find Jones.
They take Nick Lane over the Bridge to Walter's lab, and dose him with Cortexiphan and LSD. They'll wire him to Olivia, who can use her emotional bond with This Side's Nick to locate him.
Bolivia tells Olivia she likes coming Over Here, because she can see rainbows, which her world hasn't had in over 20 years. She'd hoped the healing would bring rainbows back, and still looks up after it rains.
They capture This Side's Nick, but more earthquakes happen anyway. Broyles is called to Washington, to discuss shutting off the Machine.
Nick recognizes "Olive," but he won't betray Jones, who told the Cortexiphan subjects the war between universes is happening, like they prepared for as kids. Jones claimed the quake damage on the Other Side is far worse, so they'll surrender after another offensive. Olivia says Jones lied, but Nick doesn't believe her.
As Peter examines Nick's alt-universe watch/timer, he tells Lincoln it's weird to imagine never seeing the Other Side people again. But home is where the heart is, and his is here. The watch suddenly starts counting down from six hours.Nick tells Olivia how his suicidal thoughts influenced his sister, Kendra, to kill herself. Jones explained he'd become a reverse empath - his emotions were contagious. Jones taught Nick to control his feelings, and to channel his brain's untapped energy so he can protect their world. Nick eventually agrees to help, but it's a setup. As FBI troops invade a warehouse, supposedly Jones' safe zone, Nick reverse-empaths Agent Tim into harming himself and escapes.
The Fringe teams meet, 47 minutes before the next earthquake event. Broyles says Washington will support whatever they decide. Both Walters agree: Close the Bridge.
While waiting for the power to surge so Walter can shut off the Machine, Walternate confides that Peter is a remarkable man. Walter abruptly excuses himself, but Walternate follows, sitting beside him on the floor. He knows Walter's afraid Peter may disappear. He says Walter's made the decision he didn't make 25 years ago. Walter replies, I've come to accept that he's not ours. "The universe is change," says Walternate. "Our life is what our thoughts make it." Walter smiles, recognizing Marcus Aurelius' words. Walternate says the philosopher king survived a war, then dedicated himself to bettering his people. He pats Walter's arm, saying perhaps we will too. Weeping, Walter says we'll see.
Lincoln reminds Peter what he said about home being where the heart is. Looking at Bolivia, he says he thinks he's found his. Bolivia and Olivia share a moment of mutual admiration, and Olivia says keep looking up after it rains. Bolivia will.
Lincoln stands with the Other Side's team, telling Bolivia she'll have to help him find an apartment. She smiles. Farnsworth gestures farewell to Astrid.
The overload's complete, with about 11 minutes till the earthquakes. Walter flips the switch. The room shakes . . . and the Other Side's Fringe team disappears.
But Peter's still there. Walter goes to him and says, "I think I shall miss them, more than I imagined."