
So Peter starts to tell his side of the story — our side, as viewers, really: there are two universes, and the one Over There is dying which means they both are. Olivia wonders how he knows this as Peter continues that Walter built a Machine in order to create a bridge between the universes. At this point, Walter is shaking his head. Peter tries to go on that he, Peter, was the power source for the Machine — only he can activate it.
“There is a Machine,” interrupts Walter, “but I didn’t build it!” And he looks up and hands Peter the list of questions from Broyles. He doesn’t know who Peter is or why he’s claiming to be Walter’s son. Peter very gently confirms with Walter that he and Elizabeth had a son who died as a little boy, and then Walter found the other universe’s version of him and crossed over to save him from the same illness. “But I couldn’t,” Walter adds, to Peter’s confusion, going on to tell him the story he told Aaron a couple of episodes ago (that the other Peter drowned in Reiden Lake).

I was going to make a "Not dead yet!" Monty Python reference, but "Not dead anymore!" doesn't have the same ring to it.
Peter blinks. And seriously, how weird would it be to hear that you’re dead? He says, “The Observer didn’t pull us out of the lake that night?” Astrid asks, “What’s an Observer?” Gah. Of course they don’t know about them. But this makes Peter start to understand — his existence was and is a paradox. He isn’t supposed to be alive, so he had to be deleted. Yet he’s back, even though he’s supposed to be dead in both universes. Peter grabs Walter’s arm as he wonders aloud about what’s gone wrong. Walter immediately flinches back and shouts, “We’re finished here!” He stands and bangs on the door, asking to be let out. Peter calls after him to wait, to help him figure this out, but Walter’s had enough. When the door opens, Olivia is on the other side and the two of them share a tense look.
Then Peter is shut back in his cell and Olivia gets a phone call. Lincoln wants her to come to the scene of the murder we saw at the beginning of the episode. The body’s translucent, as we know, and Lincoln has been monitoring police records for just that kind of case since his partner’s murder. He fills Olivia (and us) in that the owner of the house, Malcolm Truss, used to work for Massive Dynamic. He was a researcher, but he left the company 10 years ago. Olivia looks at the battered body of the guy and notes that he was tortured, so he must have had some info that the shape-shifter wanted. Then she notes that he has grease under his fingernails — something Lincoln also saw. This man worked at a garage. As it turns out, this is Mrs. Truss’s boyfriend, unlucky enough to be mistaken for her now-estranged husband. So the shape-shifter is no doubt looking for the real Dr. Truss, as are our heroes. Problem is, he’s gone off the grid.
Next scene is in “Eden, Vermont”. Outside, a man is tending to a very nice flower garden. He’s played by Arye Gross, who you might recognize from Castle or other guest roles. He’s interrupted by shape-shifter Nadine holding him at gunpoint, saying she needs Dr. Malcolm Truss’s help.
Olivia and Lincoln are in Nina Sharp’s office at MD. Linc notices that there’s a picture of Olivia on Nina’s desk, and the story comes out: after their mom died, Rachel and Olivia were going to go into the foster system, but instead Nina pulled some strings and became their guardian. Lincoln is duly impressed that they were raised by the acting CEO of one of the richest companies in the world. Nina comes it at that point and greets them. She is sad to hear from Olivia that Walter’s not dealing well with the appearance of this man who claims to be his son. Olivia brings the topic of conversation to Dr. Truss, at which Nina says, “The name doesn’t ring a bell.” Heh. Get it? Bell? But she finds his file and puts it up on the screen: the project he was working on that seems most likely to be of interest to a shape-shifter was cellular replication, copying the genetic material of healthy cells and using it to replace damaged ones. It was just theoretical, however, because Bell shut it down for ethical reasons. (The viewers, once again, go Bwuh?! This time it’s at the idea of William Bell shutting any project down for ethical reasons.) Olivia and Lincoln agree this could be what the shape-shifter is after.