On the Other Side, Captain Lee is buried with Colonel Broyles, Bolivia, and Lee's parents among those in attendance. Lincoln and Agent Farnsworth watch from a distance: Lincoln so Lee's parents don't mistake him for their son, and Farnsworth because she's uncomfortable at funerals. Bolivia promises the Lees that she'll bring the people responsible for their son's death to justice.
Later at Fringe Division, Bolivia visits Sharp and offers her a reduced sentence in return for her information on the identity of the mole within the DoD. Sharp refuses and says that she won't be there very long. Once Jones rescues her, things on the Other Side will become much worse.
Brian Bauer is holding a meeting with his employees and demanding to know why he and his partner had to cancel their flight to deal with one employee, Jeremy Delman, didn't make the presentation properly to their client. Jeremy doesn't have an explanation, Bauer suddenly flies up into the air, vibrates briefly, and then slams back down onto the conference table... his entire lower torso shattered.
The Fringe team is called in to investigate. As they go in, Walter comments that he tried to call Peter the previous night but didn't get an answer, and figures that Peter and Olivia were getting reacquainted. Inside, Walter examines Bauer's body along with that of his partner, who also died in the same bizarre manner. While Olivia talks to Jeremy, Walter determines that both men were apparently killed as if they had been hit by something at high velocity. However, when Walter and Astrid find lacerations on both corpses' chests which match those of a seat belt. Peter suggests that they might have been in a car crash, while Olivia gets a call from Broyles telling her that a third man, a pilot, died in the same manner but in an apartment some distance away.
On the Other Side, Agent Farnsworth informs Colonel Broyles that there has been a charter plane crash, and that the three dead passengers have counterparts on This Side that also died. As Broyles tells Farnsworth to coordinate information with their own counterparts, Bolivia comes in and informs her superior that she's narrowed the list of possible suspects to 108. Broyles warns her that it will be a bureaucratic nightmare to run surveillance on all of them but reluctantly agrees. He then asks her to coordinate with their counterparts on This Side to determine why the same three people died in the same manner.
Olivia escorts Walter through the bridge where he'll be working with the Other Side as a consultant. Bolivia and Lincoln arrive to get Walter, and Lincoln confides in Olivia that Bolivia is handling the death of her long-time partner as best she can. Olivia says that her counterpart is lucky to have him and then goes back over the bridge. As they leave the DoD facility, a guard offers Bolivia his condolences on Lee's death. As Walter examines a sign showing all of the remaining ecological "hot spots" on the Other Side, Bolivia wonders if someone could have caused the six deaths on purpose, and notes that Sharp warned them that something bad was coming. Walter admits that he doesn't know and that he and Bell were never able to synchronize objects between the two worlds.
At the Fringe Division lab, Walter confirms the vibratory pitch of one of the corpses and then takes out the severed hand of the dead man's counterpart. He checks the hand's pitch and confirms that it has the same tone, meaning that the two were vibrating on the same frequency. They check the audio recording of the crash and listen as the pilot reports that the plane is breaking up around him. Walter speculates that the person responsible hid a device onboard the plane and used it to destroy it and synchronize the three passengers.
David Robert Jones meets with one of his men, who reports that the experiment went as planned. When he asks what target he should choose next, Jones says to surprise him.
Colonel Broyles returns home to his wife Diane. She says that she and their son Chris have been entertaining Broyles' friend. When he goes into the living room, he finds Jones waiting for him. Once they're alone, Broyles insists that Jones wasn't supposed to meet him in this manner, and Jones admits that he's overdue to make a delivery of syringes to treat Chris' condition. He reminds Broyles that Chris was in constant pain until he provided the treatment. The colonel admits that he'll have to pay for what he's done eventually when he faces the consequences, and Jones assures him that love makes one vulnerable but human. As Jones leaves, he tells Broyles that he'll soon be calling on him for assistance.
In Springfield, Massachusetts, Jones' man takes a taxi ride and then gets out. A woman, Nancy Guerring, is the next person to hail the taxi.
Nancy's counterpart is out late buying pet food.
The device that Jones' man left in the back of the taxi activates and the entire taxi starts to vibrate.
Nancy is suddenly pulled violently across the floor of store. She finally comes to a halt and dies, coughing up blood.
The next day, Olivia and Peter are called to the site where the taxi crashed. Astrid is at the bridge, coordinating with her counterpart, and radioing to Bolivia, Lincoln, and Walter at the pet store. The two teams confirm that both Nancys had the same injuries and Peter finds the device inside the taxi and confirms that it contains amphilicite, meaning that Jones is involved.
Bolivia, Lincoln, and Walter tell Colonel Broyles what they've discovered, and Walter irritably snaps at the colonel when he's forced to admit that he doesn't know what is going on. Bolivia offers him a place to stay at her apartment and he agrees. When Bolivia goes to get his bag, Walter apologizes to Broyles for his ill temper and admits that he still blames himself for the whole situation since he was the one who crossed over years ago. Broyles wonders if he would do the same thing again if he had a chance. After a moment, Walter admits that originally he didn't believe he would. However, since meeting his adult son, he admits that he would do it again regardless of the consequences. Meanwhile, Farnsworth tells Bolivia that she checked out all of the suspects and was unable to confirm that any of them were the mole.
That night, Jones sets up a meeting with Broyles and gives him a small handheld device. He tells the colonel to attach it to the main control panel for the Machine. Broyles warns that the Machine is what is saving their world but Jones is unconcerned and tells him to focus on healing Chris. When Broyles goes home, he gives Chris another of Jones' injections while his son tells him about how happy he is at school now that he has a normal life. Broyles tucks his son in and says goodnight.
When Walter goes to the bathroom, he finds Bolivia drinking in the kitchen. She's going over the evidence she's gathered about Lee's murder and explains about the mole in the DoD. Bolivia also has her partner's personal effects, but admits that she can't bring herself to talk to Lee's parents until she's brought his killer to justice. Walter makes her some eggs to help with her hangover and they talk about the lack of evidence in the case. He notes that the lack of evidence is evidence in itself, and suggests Broyles might be the mole.
The next day, Bolivia goes to see Sharp in her cell and turns off the surveillance camera. She then tells the older woman that they have Broyles in custody and know that he was the mole. Unimpressed, Sharp says that Broyles was simply a pawn and that his discovery won't change Jones' plans. Bolivia points out that Jones may treat Sharp the same way that he treated Broyles, as a disposable Pawn, and that she shouldn't look to him for a rescue. Bolivia goes back to Fringe Division and tells Lincoln and Farnsworth what she's learned. Farnsworth warns them that Broyles never came to the office that morning and has shut off his subcutaneous tracker.
Broyles goes to Liberty Island with Jones' device and gets past the security man using his show-me. Its use sounds an alert at Fringe Division and Farnsworth tells Bolivia and Lincoln where they can find Broyles. They get to Liberty Island and arrive in the Machine chamber... and discover that Colonel Broyles called his counterpart and turned himself in. The colonel apologizes to Bolivia for getting Lee killed.
Later, Walter goes to the bridge and Bolivia hugs him and thanks him for his help. He tells her not to judge Colonel Broyles too harshly because he understands all too well what people will do for love. After Walter leaves, Bolivia notes that Lincoln didn't go with him and he reminds her of his promise to stay until they track down the man that killed both of their partners. As they go, he assures Bolivia that eventually the grief becomes bearable.
Colonel Broyles is locked up across the hallway from Sharp.
Walter calls Peter and Olivia to the lab and explains that Jones used the two incidents to find a common denominator, a frequency that could link both universes. When Peter points out that they can already do that, Walter warns that if Broyles had successfully attached the device, Jones could have used it to collapse both universes.