In Worcester, Massachusetts, teenagers Jill and Dave are at an abandoned warehouse getting stoned in their car. A warehouse window explodes outward and Dave decides to investigate while Jill stays in the car. He goes inside and checks out the office, where an unearthly light is glowing. Dave finds a blob of flesh on the floor surrounded by puddles of a silvery liquid. As he prods the flesh blob, a shapeshifter soldier in his natural form comes out from behind him and breaks his neck, and then uses a duplication device to take on Dave's form. He then goes outside and captures Jill, as another shapeshifter comes out to take her form.
Walter is busy rearranging the house yet again when Peter comes home and offers to help him bake a pecan pie. Walter hesitates, and contemplates a photo of himself in younger days with his wife and son. Peter notices and asks what's wrong, and Walter starts to tell him his origins in the other universe. Before he can get past explaining about life and death and science, Olivia calls to summon them to their newest case. As Walter goes to get his equipment, Peter asks him what he was going to say and Walter says it can wait.
Dave's car has been abandoned in an alleyway and Olivia and the Bishops meet with Broyles. Jill is in the car, dead, with the distinctive marks in her soft palate. As Broyles and Olivia start checking for reports of Jill having been seen elsewhere, Walter finds a joint in the car. Olivia notices that there's no lipstick on it, meaning that there was someone else in the car with Jill.
Once they track down the car's owner, the FBI finds the warehouse and discovers Dave, dead with the same puncture marks on the soft palate. They find the blob of flesh and Walter examines it, cutting it open with a scalpel. They realize that it's leaking mercury and Walter cuts it open to find an electronic device inside.
The two shapeshifters, disguised as Dave and Jill, meet Thomas Jerome Newton at a camera shop. Once they confirm who they are, Newton wonders where the third shapeshifter is when the Secretary informed him there would be three. The Jill shapeshifter explains that their comrade didn't make it.
Walter takes the flesh blob to the Harvard laboratory and determines that it's an immature embryo form of the shapeshifters, which they use to travel safely between dimensions. Olivia figures that the two new shapeshifters took the first available forms so that they could blend in. Broyles calls to tell them that the FBI has identified an electronic signal that went off at the same time as the two teenagers' deaths, and interfered with local televisions. They download the signal from the FBI FTP site and determine that there is a deliberate signal contained within the transmission.
Peter and Olivia take the recording to Brandon, who determines that it's a radio wave similar to the one generated by a solar flare, and that there was a solar flare at the same time the teenagers died. However, Brandon determines that the recording wave of the solar flare doesn't match the one that occurred. Olivia explains that it's from a parallel universe, and Brandon determines that the two signals will match the next day at exactly 3:31 pm.
Newton assigns the two new shapeshifters files on their targets, Ben McCalister and David Wu. After they have their orders, Newton tells them to meet him at the exchange point the next day at 3:20. The Jill shapeshifter questions their leader's orders, noting that they're a man short and Newton can't shapeshift without his lost device. Newton quickly puts her down, telling her that he'll take care of Mr. Verona and she should follow orders and take care of McCalister.
At a bank in Chestnut Hill, Massachusetts, Ben McCalister comes out to his car. The Jill shapeshifter approaches him and asks for directions, and then shows him a photo of himself. As he realizes something is wrong, she attacks him.
At the lab, Peter discovers that Walter is out looking at cars and attempting to stir up his memories that Newton took about the creation of the doorway. Peter finds Walter's family photo and talks to Olivia. He thinks that Walter has been acting strangely over the photo because he has finally decided to talk about how Peter's mother died. Peter tells Olivia that the only time he heard from Walter after he was committed to St. Claire was when he called to tell Peter that his mother had died in a car accident. Peter eventually learned that she killed herself, and that Walter tried to protect. Now, he figures that Walter has decided to tell him the truth. Uncomfortable, Olivia avoids telling him the truth. Walter comes in and informs them that he has an idea to activate the shapeshifter, and sends Astrid to get electrical equipment... and a fresh corpse.
At the bank, Newton meets with the shapeshifter that has now taken McCalister's form. They briefly discuss Verona, and Newton says he has the situation under control. They then go to the safe deposit vault and use a device to pinpoint a specific location in the floor. Using acid, they create a hole and start to place a small cylindrical object inside. When a teller comes down, "McCalister" conceals the hole and tells her to go back upstairs. Newton tells the soldier to make sure the device is undisturbed and leaves.
Walter wires up the embryo and explains that he thinks he can use electricity to jump-start the embryo's maturation process. Once it grows to maturation, they can use Newton's recovered device to allow it to take the shape of the fresh corpse. They feed it power in increments and blow out most of the fuses, but the embryo activates and matures into a shapeshifter. However, it's badly crippled and Walter realizes that he damaged it when he cut into it earlier. It seems to recognize Walter and grabs his arm, and then asks for help. It tells them to find Newton and Daniel Verona. Olivia tries to get more answers, but it simply tells Walter "I'm sorry" and dies.
Olivia takes a FBI team to find Verona as he leaves his home. Newton watches them and comes up with a new plan. He calls 911 and tells them that there's a heart attack victim nearby, and then takes a pill and collapses, clutching at his chest.
Olivia takes Verona to FBI headquarters, where technicians take blood samples to confirm that he's not a shapeshifter. Broyles checks Verona's background and determines that he's a medical examiner at Boston General.
At Boston General, Newton is brought in, seemingly dead. However, once he's alone he revives in the morgue, figures out where to place another of the cylindrical devices, and activates it.
Peter and Walter are at home and Peter insists that Walter gets some sleep after two days. Walter is still blaming himself for the shapeshifter's death. Peter calls him Dad and Walter is touched, and Peter realizes what he's said. Walter gets an idea and calls Olivia. When she arrives at the Bishops' home, Walter explains that he and Bell used three harmonic rods in an equilateral triangle to send the car through to the other universe. However, Newton has the advantage that he has agents working in both universes. Activating both sets of harmonic rods at the same time, at the same place in each universe, they can safely transition someone over from one dimension to another. Now they have ten hours to figure out where Newton is establishing his triangle.
The Dave shapeshifter, in the form of electrical worker David Wu, climbs a power pole and places the third harmonic rod in a conduit box.
Olivia, Walter, and Peter get out a map of Boston and work from where Verona worked at Boston General. When they get word that McCalister's corpse has turned up, they conclude that the bank is the second point of the equilateral triangle. That gives them two possible third points and they figure out the two center points of the triangle. One of them is a bridge on the Charles River, and Olivia remembers what Walter told her about using water to absorb the excess energy of a transition. She brings up the idea and Walter agrees, and Peter wonders where she got the idea.
At the Charles Bridge, Newton and the two shapeshifters assemble their equipment. When the police drive up to the bridge on the other side, Newton tells his soldiers to deal with them.
As Broyles sends agents to search for the harmonic rods, Olivia, Peter, and Walter go to the Charles Bridge. En route, Walter uses a laptop computer to compute an opposing sound wave which he'll transmit using a pneumatic hammer. However, Walter warns that they have to get the hammer as close to the center of the bridge as possible... and the vibrations could tear someone apart.
At the bridge, Olivia and Peter approach the police officers, and one takes out his cell phone to call in for orders. Olivia realizes that police officers wouldn't use a cell phone to make a call and shoots one of them. The other one takes cover, opens fire, and pins down Olivia and Peter. Walter drives the SUV out onto the bridge and Peter tries to go after him, but the remaining shapeshifter pins him down.
Newton activates the equipment, triggering the three harmonic rods. Walter looks down at the river as a wave of sonic energy spreads through the water. Meanwhile, Olivia provides cover fire so that Peter can get to the bridge. Realizing what's happening, Newton calls the shapeshifter and tells him to stop Walter and Peter. The soldier tries to go after them and Olivia shoots him.
As Broyles and his team arrive, Walter and Peter activate the hammer. However, the frequency recognition software fails to operate as planned. A FBI agent comes out to watch over Peter, who gets Walter off the bridge before going back to work on the software. They watch as the bridge from the parallel universe starts to materialize. As a figure from the other Earth walks onto the bridge, the sound waves disintegrate the FBI agent but leave Peter and the new arrival unaffected. Peter manages to rewrite the software and the counterpulse shatters the convergence, knocking Peter unconscious.
Peter is taken to the hospital and wakes up a day later, with Olivia watching over him. He asks to talk to Walter alone, and Olivia leaves. When Peter explains what he saw, he figures that the newcomer from the other Earth wasn't hurt by the sound waves because of his origin... and Peter was similarly protected. He tells Walter that he now knows the truth, that Walter abducted him from the other Earth, and that his mother committed suicide out of guilt. When Walter calls him, "Son," Peter says he isn't Walter's son and tells him to get out.
Newton manages to get the newcomer away to a secret base. He addresses him as the Secretary and gives him an injection to deal with the aftereffects of dimensional transit. Newton affectionately takes the Secretary's hand and assures him that he'll be okay.
Olivia arrives at the Bishop home as Walter prepares to go back to the hospital. She tells him that Peter checked himself out of the hospital hours ago and has disappeared.