As The Man From The Other Side begins, we see two teenagers who are murdered by shapeshifters. The team is called in to handle the investigation. At the scene of the crime, they discover a pod that contains the dead embryo of a third shapeshifter.
The two shapeshifters that are alive assume the teenagers’ identities and meet with Newton in a camera shop. They tell him that the third shapeshifter didn’t survive.
Back in the lab, Walter inspects the embryo well Olivia tries to decode a radio signal that may have originated on the other side. Olivia visits Brandon at Massive Dynamic, who agrees and explains that the two universes’ time lines will be completely in sync within twenty-four hours.
Meanwhile, Newton gives the shapeshifters their orders. One of them questions the validity of the plan without a third shapeshifter but Newton assures them that if it doesn’t work “The Secretary” will be unhappy so they agree to put the plan into motion.
Later at the lab, Peter realizes why Walter has been acting strange. He finds an old family photo that Walter has been carrying around and tells Olivia that he thinks his mother committed 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.
At the same time, Walter figures out a way to bring the third shapeshifter back to life. It tells the team that it was supposed to meet with Newton, and its intended target was a medical examiner named Daniel Verona, then it died again.
Newton sneaks into the morgue where Verona works by pretending to be a corpse. There, he plants a device identical to the one in the bank. At another location, one of the shapeshifters plants a third device in the electrical box of a telephone pole.
Walter shows 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, 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. 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 is OK. He activates the hammer and sees that Newtom has brought over a man form the other side.
Peter is knocked unconscious by a second shockwave and he wakes up in the hospital. He confronts Walter, asking why he didn’t die on the bridge and realizes he was from the alternate universe, shunning Walter in the process.
In another recovery room, Newton nurses The Secretary who he brought back from the other side.
The next day, Olivia visits Walter at his house and tells him that Peter has disappeared.
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