Brandon tells Walternate that they've isolated half of Peter's genetic profile from his grandson's DNA. That should be enough to activate the machine. And Brandon's proud to help save their universe. Walternate muses that Oppenheimer saved us too, but at what cost? He quotes Oppenheimer quoting the Bhagavad Gita in describing the first atomic bomb detonation: "Now, I am become Death, the destroyer of worlds." But, adds Walternate, we really will destroy their world to save ours. May God have mercy on us.
Sam Weiss, the mysterious bowling-alley manager, detects an energy disturbance. He goes to a padlocked cabinet. Sam removes a Newton's cradle. He doesn't touch the line of hanging silver balls, but they start clicking back and forth. He's not pleased.
At the Bishop house, Olivia wakes up next to Peter. In the hallway, she surprises Walter . . . who's naked, except for fuzzy slippers. He delightedly says that he'll make another mushroom frittata. Informed of this, Peter laughs. Walter always cooks naked on Tuesdays. Olivia says this is her favorite time of day, sunrise - when the world is full of promise. Their phones ring.
On a vast dirt patch torn through an upstate New York pasture, Broyles tells Olivia and the Bishops that two men and more than 500 sheep just disappeared, around 6:05 a.m. Walter finds evidence of a vortex. It's his worst fear: Their world is breaking down. Nina phones Broyles from the Massive Dynamic hangar housing the machine. Somehow, it came on by itself at 6:02 a.m. - right before the vortex opened. The machine caused this.
At Harvard, Peter asks if he's the power source, how could the machine switch on without him? Walter explains its electromagnetic field indicates quantum entanglement. Walternate turned on his machine and triggered a sympathetic response from this one. But how? More incidents are happening, and they have no way to stop it. Walternate's won.
Bolivia's out with three-week-old baby Henry when she gets a Fringe call about a Class 10 event at the DoD complex. But the Secretary orders Fringe to stand down. Bolivia visits him and mentions the weapon he told her about, the one that could destroy the Other Side. Did he activate it? He stonewalls. When she argues that his son is Over There, he icily says that Peter chose to leave. Walternate gave up his son, so Bolivia could keep hers. Dismissed.
Thanks to Olivia's knowledge of the Other Side, Nina begins tracking irregularities that can help them predict anomalies. Olivia leaves for MD, telling Peter that there must be a way to stop the machine. As Walter brainstorms desperately, Peter says they both know there's another way.
Maybe Peter can turn it off. Maybe that's what the drawing means. Walter pours two drinks from a flask. He says Peter could die. If we do nothing, says Peter, we'll all die. Walter quotes the Observer: "Give him the keys and save the girl." He has to sacrifice Peter to fix things. Peter thinks this is what he's supposed to do, but he needs Walter's help. Father and son clink glasses.
Nina tells Olivia more about Sam Weiss. He was a longtime associate of William Bell, who advised Nina to trust Sam implicitly. He knows a lot about the machine. But the bowling alley's closed, and Sam's disappeared.
In Saratoga Springs, New York, a young couple sees strange lights in the sky. Sam sees them too. He peers through a window-like device and records data for some elaborate calculation.
Bolivia leaves baby Henry with Lincoln - the only one she trusts - and heads to the DoD. She plans to commandeer whatever mechanism Walternate used to cross over, so she can ask Peter for help. But she fails and lands in the brig.
Olivia finds Sam's apartment in Boston, empty. At the hangar, Peter's ready to enter the machine. Walter fusses, but it's time for him to let go. And for Peter to face his destiny. Astrid holds Walter's hand as Peter rides the lift up to the machine, touches it . . .
. . . and is thrown violently to the floor!
At the hospital, Astrid tells Olivia that the machine seemed to be protecting itself. Peter is unconscious but stable, with no apparent brain trauma. They're hoping he comes around soon. In the chapel, an agonized Walter tells God he was willing to let Peter die. He's changed. That should matter. But his crimes are unforgivable. So, punish him. "But I beg you" - he brings his hands together pleadingly - "spare our world."
Olivia stares at a light creeping across the waiting room floor. She goes outside. It's sunrise. "Hello, Olivia," says Sam Weiss. He asks her to take him to the machine. Trust him. They don't have much time.
Walternate visits Bolivia's cell. She was willing to leave her son behind, to risk her life, for what she perceives is the greater good. They aren't that different. She doesn't see how killing billions could possibly be for the greater good. He retorts she still has the luxury of her ideals; he has to be pragmatic. Anyone else would rot in the stockade for treason, but she IS his grandson's mother. She'll stay here for her own good, until this is over.