When two teenagers are murdered by shapeshifters from the alternate universe, the Fringe team is called in to handle the investigation. At the scene of the crime, the team discovers an unhatched pod that contains the lifeless embryo of a third shapeshifter.
The two live shapeshifters, now assuming the teenagers' identities, meet with Newton in a camera shop, and inform him that the third member of their party didn't survive.
In the lab, Walter inspects the shapeshifter embryo, and Olivia attempts to decode a strange radio signal that may have originated from the other side. Olivia pays a visit to Brandon at Massive Dynamic, who confirms her hypothesis and goes on to explain that the two universes' timelines will be completely in sync within twenty-four hours.
In the typewriter shop, Newton gives the shapeshifters their orders. One of them questions whether their plan will work without a third shapeshifter, and Newton says that if it doesn't work, his boss (known as "The Secretary") will be very displeased. They part ways and begin setting the plan into motion.
Back at the lab, Peter has a revelation as to why Walter has been acting so strangely towards him. He finds an old family photo that Walter has been carrying around lately, and tells Olivia that he thinks Walter wants to come clean about the way his mother really died, which was a suicide.
Newton goes to a local bank, where one of the shapeshifters has assumed the identity of a manager named McCallister. They go down into the bank vault and embed a small device into the flooring.
Meanwhile back at the lab, Walter figures out a way to catalyze the embryo and momentarily bring the third shapeshifter back to life. Before it dies, it tells the team that it was supposed to rendezvous with Newton, and its intended target was a medical examiner named Daniel Verona.
Pretending to be a corpse, Newton sneaks into the morgue where Verona works, and plants a device identical to the one in the bank. Somewhere across town, one of the shapeshifters plants a third device in the electrical box of a telephone pole.
At the lab, Walter demonstrates to Peter and Olivia how he and William Bell were able to transport a car into the other universe by making it vibrate at the proper frequency. He suggests that Newton may be trying the same thing by setting up three carefully positioned harmonic rods throughout the city. With two of the rod positions known (the morgue and the bank), Peter pulls out a map and triangulates the center of Newton's portal... it's a bridge on the Charles River.
The team rushes over to the bridge, and after a shootout with the shapeshifters, Walter prepares a pneumatic hammer that will nullify Newton's frequency. The hammer doesn't work properly though, and Peter jumps in to help. Peter tells everyone to clear the area, and Olivia pulls Walter back to a safe distance. Newton turns on his harmonic rods, and a shockwave rips across the Charles River. A nearby FBI agent is torn apart by the blast, but Peter miraculously remains un-phased. He succeeds in activating the hammer, but not before getting a glimpse of what Newton brought over... he sees the lone figure of a man.
Peter is knocked unconscious by a second shockwave, and he wakes up in the hospital. Walter comes in to greet him, but Peter receives him coldly. Peter confronts Walter, and explains that when he didn't die on the bridge the same way the FBI agent did, he realized he was from the alternate universe. He disowns Walter, and tells him he'd like to be left alone.
In another recovery room on a different side of town, Newton nurses the man he brought over from the other side... it's "The Secretary."
The next day, Olivia visits Walter at his house and informs him that Peter has disappeared.