In Worcester, Massachusetts, two teenagers are getting stoned in their car near an abandoned warehouse. The boy, Dave, feels something shake, but the girl dismisses his momentary concern. A window in the warehouse suddenly explodes and the boy insists on investigating. Inside, glowing lights come from an office and another window explodes as a blob of flesh forms on the floor. Dave enters and prods it, and a shapeshifter comes up behind him, snaps his neck, and places a duplication device in the boy's mouth. Finally he takes on the teenager's form.
Outside, the girl asks "Dave" what's going on as he gets in the car. Another shapeshifter emerges from the warehouse and "Dave" grabs her.
Peter comes home to find Walter rearranging things yet again. As Peter offers to bake a pecan pie with him, Walter notices a Bishop family photo and hesitates, and then tells Peter he has to tell him something. He starts to explain about life and death, but Olivia calls to tell them they have a case. A relieved Walter goes to get his field kit. Peter asks what he was going to say, but Walter dismisses it as something that can wait.
The team meets Broyles at where Dave's car was abandoned. Jill is dead, her neck broken, and there are three puncture marks in her palate. Realizing that shapeshifters are involved, the team begins a check for anyone using Jill's appearance. Walter finds a joint but Olivia realizes there's no lipstick on it, meaning someone else was present.
The FBI soon locates the warehouse and find Dave, dead and lying in a puddle of mercury. They confirm that Dave has three puncture wounds in his palate. They find the flesh blob and Walter starts to cut into it as Olivia wonders why the shapeshifters would want two teenagers. Mercury leaks from the incision and Walter digs inside to find a metal box.
The shapeshifters disguised as Dave and Jill go to a camera shop to meet Newton. Once they use passphrases to identify who they are, Newton notes that the Secretary said there would be three of them. The Jill shapeshifter explains that the third one didn't make it.
In the lab, Walter examines the specimen and concludes that it's an embryo, and the shapeshifters use it to travel between universes. The one they have failed to mature properly. Olivia realizes that the two remaining shapeshifters needed human forms to blend in, and the teenagers were in the wrong place at the wrong time. Broyles calls and sends them a video file taken from a television near the warehouse. Several neighbors report an electronic disturbance at the time of the teenagers' deaths. There is some kind of repetitive signal on the recording, and they take it to Brandon at Massive Dyanmic for analysis.
At his lab, Brandon explains that the signals are math formulae and the radio wave is similar to one given off by a solar flare. Massive Dynamic detected increased solar activity at the same time. However, the two radio waves, the Sun's and the broadcast, don't match. When Olivia suggests a parallel universe, Brandon admits that the discrepant time flow could account for the different radio waves. The computer determines that the two universes will be in sync at exactly 3:31 p.m. the next day.
Newton hands out files on their two targets, McCalister and Wu. He tells them to rendezvous at 3:20 p.m. the next day at the exchange point. The Jill shapeshifter wonders why they're still going through with the plan when they're a man short and Newton doesn't have a shifting device. Newton assures her that he'll handle Mr. Verona and she needs to complete her part of the plan.
In Chestnut Hill, Massachusetts, McCalister emerges from a bank and the Jill shapeshifter approaches him and asks for directions, luring him away from his car.
Peter returns to the lab and Astrid informs him that Walter is out trying to stir his memories of what he told Newton about opening a doorway between universes. As he looks through Walter's books, he finds the photo of the family that was at the house. Peter then checks in on Olivia, who is going over a list of state and federal events in the area. He suggests that Walter has been acting strange because he wants to talk about how Peter's mother died. Peter explains that a month after Walter was locked up, he called to tell Peter that she died in a car crash, but actually his mother committed suicide. He figures that Walter was trying to protect him, but has decided to tell him the truth. Before Olivia can say more then that Walter loves him, Walter comes in and says he's come up with a way to find the shapeshifters. He sends Astrid to get electrical supplies and a fresh corpse.
Newton goes to the bank and meets with the Jill shapeshifter, now disguised as McCalister. It asks if he's figured out what to do about Verona, and Newton says he has a few ideas. They go to the safe deposit vault, use a detection device to pinpoint a location, and create a small hole in the floor with acid. A teller comes in to get McCalister's approval on some paperwork, and they hastily cover up the hole. Once she leaves, Newton tells the soldier to handle the rest, gives it a small cylindrical device, and tells it to make sure the Device isn't disturbed.
Walter hooks up his electrical equipment to the embryo, and believes that they can jump-start its maturation process. He needs the corpse so the shapeshifter has a form to take on so they can question it. Walter begins and they gradually feed more power into the embryo. A fuse blows out and the embryo starts to move as the humanoid figure within frees itself. However, it collapses and Walter realizes his earlier incision may have harmed it. He gets the palate device to let it take on a human form, and it grabs his arms and begs them to help it. It asks them to contact Newton, and mentions the name Daniel Verona. As they try to find out what it knows about 3:31 p.m., it takes Walter's hand and says that it's sorry, and then dies.
Olivia and a FBI team take Verona into protective custody. Nearby, Newton makes an anonymous call saying there's a heart attack victim at his location. He then takes a pills and collapses.
At FBI headquarters, the technicians confirm that Verona isn't a shapeshifter. Broyles confirms that Verona is a medical examiner working at Boston General.
At Boston General, Newton's seemingly dead body is taken to the morgue. Once he's alone, Newton revives and uses his tracking device to pinpoint his location. He then takes out a cylindrical device and activates it.
At their home, Peter notes that Walter has been awake for two days and needs some rest. Walter is blaming himself for killing the embryo shapeshifter and Peter tells him to get some rest and calls him Dad. Walter is surprised and touched to hear him say it, and so is Peter. Walter gets an idea about Newton's plan and they call Olivia. Once she's there, Walter explains that he and Bell used three harmonic rods to create a doorway between universes. Newton has agents in both universes and can use two sets of harmonic rods to make an exchange when the two words are in sync. Walter has no idea what Newton plans to bring over, but they have ten hours to figure out where the center of the triangle is located.
The Dave shapeshifter, having taken on the form of power company worker David Wu, plants the third harmonic rod in a transformer box.
Walter, Peter, and Olivia try to work out where the harmonic rods are, and figure that Verona is connected to one of the three points. Astrid tells them that the police have found McCalister's corpse. They use the bank as the second point, which tells them that the third point is in one of two locations on an equilateral triangle. That gives them two possible center points. When Olivia realizes one of them is a bridge on the Charles River, she remembers Walter describing how he used a lake to absorb the excess energy when he traveled to the other universe. She selects the bridge and Walter agrees. Peter wonders how they came to that conclusion.
Newton and his two soldiers are at the bridge with their equipment. The police arrive and Newton tells the soldiers to deal with them.
Broyles coordinates a search for the harmonic rods while Olivia, Peter, and Walter drive to the bridge. Walter tries to come up with a way to stop the process by projecting an opposing sound wave via a pneumonic hammer. They have to get the hammer as close to the center of the bridge, but Walter warns that the sound waves necessary could easily tear a man apart.
They arrive at the bridge and Olivia and Peter go forward. The two police officers stop them, and Olivia realizes that their shapeshifters when one uses a cell phone to call headquarters. She kills one and the other takes cover. With time running out, Walter drives the SUV onto the bridge. Pinned down by enemy gunfire, Peter is unable to go after him.
Walter drives onto the bridge while Newton activates the convergence device. In the three locations, the harmonic rods activate. A wave of sonic energy sweeps across the bridge and the water below.
Peter has Olivia cover him while he runs toward the bridge and insists on helping Walter. Newton calls and tells his remaining solider to dispose of them. Olivia guns him down as he tries, and Broyles and his agents arrive. On the bridge, Walter and Peter activate the hammer but there's something wrong with the frequency recognition software. Peter insists that they get Walter off the bridge while he reprograms the software and a FBI agent keeps guard.
As the convergence begins, the bridge in the alternate universe begins. As Peter struggles to fix the program, the FBI agent is disintegrated by the sound waves, while a figure appears on the second bridge. Peter finishes just in time, stopping the convergence before the figure can fully arrive. Sonic waves knock him unconscious.
Later, Peter wakes up in the hospital with Olivia watching over him. He asks to speak to Walter alone. Peter then tells Walter that he saw the man on the bridge, and wonders neither he nor Peter were affected. He realizes that Walter brought him over from the other universe, and that his mother committed suicide because she knew the truth and couldn't live with the guilt. Peter angrily says that he's not Walter's son and tells him to leave.
In a hidden base, Newton tends to the newcomer, the Secretary, and treats him for the injuries sustained due to dimensional transit. He sedates him and takes his hand to reassure him.
Later, Walter insists on going to the hospital to see Peter. Olivia arrives at the Bishop home and tells Walter that Peter checked himself out of the hospital three hours ago, and there's no sign of him.