Back in the alternate universe, Fauxlivia reunites with her boyfriend Frank at the airport. Meanwhile, a grey-haired scientist, Dr Anton Silva, sits at the airport bar and switches his drink with a fellow patron. Having ingested Silva’s concoction, the seriously-ill patron stumbles to the toilet, but is eaten from the inside-out by flesh-eating bugs. Meanwhile, as she arrives home with Frank, Fauxlivia explains that Lincoln has been placed in charge of Fringe division in Colonel Broyles’s absence.
The next day, the Fringe team discover the airport victim’s corpse and recover one of the bugs. Fauxlivia and Charlie visit Foster, a female scientist with a crush on Charlie, and she identifies the bug as a skelter beetle, a parasitic creature that lives exclusively in sheep. Since sheep died out ten years ago in the alternate world, the beetles were believed to have died out with them. Elsewhere, Dr Silva conducts an experiment on one of the beetles he recovered from the airport victim’s corpse and is frustrated when he cannot synthesise a particular enzyme from the bug.
At Fringe headquarters, Lincoln recruits Frank to help out with the case. Frank confesses in confidence that he is planning to propose to Fauxlivia, but the loud-mouthed Lincoln instantly relays the news to her. Meanwhile, Fringe division puts out a public appeal for information on the bugs and receives a tip from an old colleague of Dr Silva, who reveals that the scientist was an expert on skelter beetles and has conducted experiments on them in the past. At a local café, Silva infects another innocent victim with the parasites and later collects the bugs from his corpse. When the Fringe team examine the remaining bugs sometime later, they notice that the beetles look different and have become larger.
Meanwhile, at the Department of Defence, Brandon informs Walternate that they have made a breakthrough in the Cortexiphan trials and shows him footage of a test subject displaying telekinetic abilities. Brandon explains that the successful test was performed on the youngest subject yet and suggests experimenting on children, but Walternate refuses. That night, Walternate opens up to his lover, pondering his recent decisions and lamenting the loss of Peter, but she insists that he is a strong man and that he will get Peter back eventually.
Arriving home, Fauxlivia is filled in by Frank on his latest research. He explains that Silva almost cured avian flu using an enzyme in the skelter beetle, and, now that sheep are extinct, he is likely trying to modify the bugs to live in humans. As Fauxlivia prepares to report back to headquarters, Frank surprises her by proposing early and she happily accepts.
Meanwhile, Lincoln researches the specialist equipment that Silva used to conduct his experiments and tracks the scientist down to a Brooklyn warehouse. He and Fauxlivia split up to explore, but Silva locks Lincoln in a freezer room, while Fauxlivia falls through the unsafe floorboards into the room below and is knocked unconscious. When Fauxlivia wakes up, Silva explains that the gestation of a new queen beetle has already begun. Lincoln escapes from the freezer room and confronts Silva at gun-point, while a sickly Fauxlivia is rushed to the hospital, apparently infected by the parasite.
As Fauxlivia is taken away in an ambulance, Silva reveals that she is not the host of the queen beetle, he is. The creature eats its way out of Silva’s neck and he dies, content that he will now be remembered for his scientific discoveries. Meanwhile, Frank gives Fauxlivia an ultra-sound scan in the ambulance and learns that she is not infected, but that she is pregnant. At the hospital, Fauxlivia is forced to confess that she is only six weeks pregnant, and since Frank has been away for longer, he realises that he is not the father and angrily departs.
That night, Walternate receives a phone call from Brandon, who reveals that a new opportunity has arisen to bring Peter back to his original universe. Walternate visits Fauxlivia at her now-empty apartment and reveals that he knows about her pregnancy. He assures her that her position in Fringe division is safe, telling her: “After all, you are the mother of my future grandchild,” confirming that the real father is Peter Bishop.