When they get there, he tells them that he thinks he's worked out what's happened to the town. Upon examining Teresa's blood, he found ninety-two chromosomes in her DNA, twice the genetic material any human should have. Olivia wants to know how that's possible, and Walter starts explaining that he and Belly once combined a tiny portion of their universe with the alternate universe (no explanation on how that happened) in a goldfish bowl in the lab, and the effect on the physics -- gravity, electromagnetic fields -- was catastrophic. Peter sums it up: "What you're saying is the two universes merged together somehow?"
Walter draws a Venn diagram on the blackboard, with each circle representing respective universes, and the overlapping portion representing Westfield itself. That's where they're trapped. Peter's starting to follow along, figuring that people are going insane because they're merging with their doppelgangers. "Can you imagine being flooded with years and experiences and memories that were not your own?" asks Walter. Olivia asks if it can be reversed, and Walter says it can't, that the damage is done. This, understandably, freaks Olivia and Peter out, surprising Walter until he remembers to tell them that Olivia's blood was fine. "You left that part out," says Peter, as Olivia practically collapses in relief. Walter explains that as with the three of them, Cliff and other survivors don't currently have doppelgangers in the town in the alternate universe. Olivia relays the information about Cliff turning down a job offer in Philadelphia, and Peter figures that Cliff in the other universe must have taken it and moved his family. He asks Walter if this could happen naturally, and Walter doesn't see how, because when he and Belly merged just a tiny portion, it required tremendous energy. "I can't imagine an energy source that would merge an entire town."
Peter's already got it figured out, and asks if it could be amphilicite. Walter, following his thinking, says that would do it. Olivia wants to know, if this is what David Robert Jones wanted the amphilicite for, why he's doing it, but Walter says there's a more pressing concern: "The effects I have just described, they are just Phase 1." Olivia asks what Phase 2 is, and the school immediately shakes, like it was just hit with a miniature earthquake. Cliff hobbles in to tell Olivia that she needs to see this, and everyone goes up on the roof, and look at the town, which is blurry and shimmering in spots. As the watch, a water tower winks out of existence. "That is Phase 2," says Walter grimly.