Peter is transported under heavy guard to the Boston Federal Building, where Broyles and several agents escort him to . . . a holding cell.
At Harvard, Olivia tells Walter the mystery man will only talk to him. He's saying his name is Peter Bishop, and that he's Walter's son.
The human shapeshifter who took Nadine Park's identity (in "Neither Here Nor There") has killed a woman named Karen and assumed her form. Confronting a man in Karen's house, she demands his files.
At HQ, Broyles says DNA tests show a 99.7 percent probability that the stranger is related to Walter. Walter theorizes he's another version of Peter from a third universe, who didn't die as a boy.
Walter meets with Peter, who asks for help in figuring out why no one remembers him. He says Walter built a machine to form a bridge between worlds, and Walter huffs that HE didn't build it. Peter's more surprised when Walter says he did cross over to save the other Peter, but the boy drowned. He asks, the Observer didn't pull us out of the lake that night? Outside, the team wonders what an Observer is. Peter realizes that he was supposed to die in both universes. When he didn't, he became a paradox. So he had to be deleted. But if I'm already dead in both universes, he asks, then how am I here? And why am I back? He grips Walter's wrist, but Walter pulls away and flees.
Lincoln calls Olivia to the crime scene at Karen's. Clearly, there's another shapeshifter. The house belongs to Dr. Malcolm Truss, a biotech scientist who left Massive Dynamic ten years ago. The dead man's been tortured, so the shapeshifter must have wanted information. Except he isn't Dr. Truss - he's the boyfriend of Karen, Truss's estranged wife.
Meanwhile, the shapeshifter, back in Nadine form, finds the scientist. She points a gun at him and says that she needs his help.
As Lincoln and Olivia wait in Nina Sharp's office, Olivia explains that she and her sister moved in with Nina after their mother died. Nina arrives and asks how Walter's doing. Not well, says Olivia, but they're here about Dr. Malcolm Truss.
Nina recalls Truss' project on cellular replication. It was designed to heal extensive tissue damage, such as that from burns or cancer, by copying genetic data from healthy cells and using it to replace damaged ones. But William Bell shut it down due to ethical concerns.
Peter hacks his cell intercom and eavesdrops as the team discusses the mysterious tech retrieved from the shapeshifters. He interrupts, explaining they're memory disks. He knows from his decryption work that they have three sections: cognitive functions, biochemical functions, and mission objective. Over Broyles' objections, Lincoln asks if Peter could decrypt this one.
Nadine makes Malcolm drive. She claims that she had stage 4 melanoma until, thanks to his research, some people cured her - people who want him to continue his work. She says the procedure didn't fully take, and he agrees to help. In a warehouse lab, Malcolm bitterly recalls how Bell shut him down and told him, "Some things are not ours to tamper with; some things are God's." Later, when Malcolm injects Nadine with a serum to fix her skin, she suddenly shapeshifts into Karen! She resumes Nadine form and forces the distressed scientist to try again.
Nina visits Walter, hoping to heal their longtime rift. He recalls how Nina begged him to stop at the lake. He blamed his son's death on her interference, but she was right - he'd crossed the line. He says that he saw the eyes of his boy in a man's face, and it gave him indescribable joy. But he doesn't deserve joy. Nina says maybe this is a second chance.
Peter discovers the new shapeshifters can switch between every identity they've ever assumed, and they replicate every strand of a victim's DNA. So, if they perfect this tech, the only way to expose one will be by surgically hunting for a memory disk. Also, the disks broadcast coordinates, like a shapeshifter tracking device. There's a blip by the port: their target. Olivia and Lincoln move out.
An FBI team bursts into the warehouse. Nadine starts shooting, grabs Malcolm's latest serum, and heads for the roof as Olivia pursues. Lincoln helps Malcolm while an injured agent tells Olivia the suspect jumped into the water. But the injured agent is really the shapeshifter, who escapes.
At HQ, an agent named Jill says, "Agent Dunham, I have those hourlies you asked for." Olivia puts the files on a desk. She speaks with Lincoln, who leaves. Then Jill walks up: "Agent Dunham, I have those hourlies you asked for." Confused, Olivia says you already gave me the - but the files aren't on the desk. Weird.
Walter puts his hands on Peter's face. He's often tried to imagine how his son would look as a man. He pulls back and declares that Peter was sent to tempt him, to see if he would repeat past mistakes. Walter can't help. He tried to help a boy, a version of his son, 25 years ago. "But that boy was never my son, and neither are you." He leaves Peter alone, helpless.
At a train station, Nadine injects the serum to stabilize her form. She removes an old-fashioned portable typewriter from a locker and types, "Status Report: Doctor Truss Located. Serum Synthesized Successfully. It worked." The machine types a response: "Understood. Begin preparations. We're sending the others."