In Milton, Massachusetts, a man gets a pickaxe out of his bag and turns to confront the family, who he has tied up and gagged. He then turns up the TV and approaches the family.
In the basement, two men are digging up the floor. They finally remove a strange box. Blake wonders what's in it, but Mitch warns their curiosity got the better of them in Texas. Nonetheless, he agrees to take a pick. The light bulb flickers and both men become comatose, their noses bleeding. Mitch's cousin Joe comes down and closes the box, and then runs out with it. Before he goes, he looks at the family, who are in the same state as his cousin and his friend.
Bolivia meets with Newton and they review Olivia's files. He tells her to read up on pop culture and warns her not to be taken in, and then assures her that he hired a team and sent them to the site as she requested. Newton removes her tattoo and hints at insubordination, and Bolivia reminds him that it's operation and she's in charge.
At Harvard, Astrid is reading Bell's obituary while Peter briefs Broyles on the fact that Walternate is assembling an ancient device and needs Peter as a key component. Broyles asks Walter why it would be configured for Peter, but Walter isn't willing to aid them getting a device that can kill millions. He leaves for the market, walking past Bolivia as she arrives. Once Walter is gone, Broyles asks Peter to help get Walter focused. Peter wonders if they shouldn't be working on the device, and then leaves with Bolivia.
Peter and Bolivia go to a bar for drinks, and Bolivia suggests that he convince Walter to work on the device. When she comments like she like a song on the jukebox, Peter is surprised and notices that she's never expressed an interest in music. Bolivia says that she's reconsidered her life since being on the Other Side, and invites him to dance. Peter admits that it was strange being with the other Olivia and notes that she made a sexy redhead, and says that she still feels real.
The Fringe team is called to Milton to investigate the family's deaths. Walter notes that their blood is too light, suggesting spinal fluid is mixed in. Neither of the men in the basement have ID, and Walter hypothe they were in a vegetative trance before they died, and wonders if the box might have walked off on its own.
The next day, Bolivia tells Newton what happened in Milton, and he confirms that he only hired two men. They figure the third man is immune, and that they need to find him.
Joe studies the closed box.
Walter and Astrid begin to remove the brains from the two men. Peter comes in and Walter wonders if he's underdressed, and Astrid assures him that he's fine. They go to Massive Dynamic and meet with Nina. Walter expresses his condolences for Bell's death and impulsively. They gather for a reading of Bell's will. He leaves her a memento of their time together in Tuscany, and Walter an envelope with a letter. Afterward, Peter asks what Bell left Walter, but he refuses to tell him. Broyles calls and wants to know why they're not at Blake's apartment, since he called and told Bolivia about it when they identified him by his fingerprints.
Bolivia is searching Blake's apartment when Peter comes in. She apologizes and says that she didn't call him so that he'd stay with Walter instead. Peter realizes that Blake has a friend living there, and he stays to do a onceover while she goes outside. As she makes a call in the alleyway, Joe drives by and sees her, and realizes that she's an agent. As she calls Newton to tell him to come to Joe's apartment, Joe writes down her name despite the fact he couldn't hear it at that distance. The box is on the seat next to him.
At Harvard, Astrid finds Walter contemplating the damaged brain taken from one of the dead men. He angrily pulls off his gloves and shows her the safety deposit key in the box. The letter simply says, "Don't be afraid to cross the line." Walter admits that he was the cautious one, and Bell went to the Other Side and saw what Walter did. He doesn't understand why Bell would tell him to be less cautious. When Astrid tells him that he has to tell Peter what he did to save him, Walter insists that he's waiting for the right moment. Instead of responding, Walter realizes that both men suffered severe damage to the inner ear, and realizes what's happened.
Walter has Peter and Astrid help him get his monitoring helmet on it, and he demonstrates how music affects neurons. He then explains that certain ultrasound waves could induce a vegetative trance and damage to the inner ear. Walter suggests that the third man might have needed a sophisticated pair of headphones to protect himself, and Peter contacts Broyles to have him monitor the city for ultrasonic activity. As he goes, Astrid tells Walter to talk to him.
Bolivia is at home reviewing Olivia's case files when Joe arrives at her doorstep. She holds him at gunpoint and tells him to put the box down. Bolivia quickly realizes that he's deaf, which protected him from the box's effects.
Walter approaches Peter and tries to explain, even when Peter wants to leave. He tells Peter about how when his Peter died, he lost all hope. The only thing that kept him alive was his wife, and the window into his world, but he refused to cross over because it was too dangerous. However, when Walter saw Peter dying, he took the chance. Peter reminds him that he kidnapped him, and Walter admits that he didn't plan it that way. Now he realizes that what he did was wrong. Peter says he can't talk about it yet and leaves.
Newton comes to Bolivia's apartment and she explains that Joe saw her badge and figured he was turning it over to the authorities. Newton offers to kill Joe, but Bolivia tells him to do his job. Once he leaves, Bolivia puts a silencer on her gun and then shoots him from behind.
As Bolivia hauls the body away, there's a knock on the door. Bolivia checks and sees that Peter is outside. She asks for a minute, fakes getting out of the shower, and hides Joe's corpse in the bathroom. Once she lets him in, Peter tells her what Walter told him, and how he can't bring himself to accept Walter's apology. Bolivia says she understands, but Peter points out that Walter all but destroyed the other world. Bolivia asks him about himself, and he wonders about his connection to the machine, and if he'll become the destroyer of a world. Bolivia notices Joe's blood seeping out from under the door and starts kissing him as a distraction.
Newton goes to a train station and sits down on a bench. A small man notices it and asks what's in it, and he says it's better to imagination. He then pays the man to watch the box while he goes to the restroom.
Bolivia's and Peter's phones ring before they can go any further. They go to the train station where Broyles informs them they have five more trance victims. The small man took the box down the tunnel to the next station, and Broyles prepares to send a bomb squad to stop them. Peter warns that the box isn't a bomb, and offers to go after it. Walter warns against it, but Peter realizes he knows a way to deaden the ultrasonics. Walter admits there is, and asks Bolivia for her gun. Bolivia fires two rounds, ones past each ear to deafen him, and Peter goes into the tunnel. He follows a trail of dead rats and finally finds the man in the same coma. The box is lying nearby. The man's head explodes and Peter quickly picks up the box and closes it. He then recognizes it as a piece of the weapon from the other side.
Peter tries to close the box but discovers it was broken by the drop. He works to disarm the device before his hearing returns. With time running out, Walter insists that they send someone else in. Bolivia hears a coming train and runs off after Peter.
Peter cuts the power to the device and feels the vibration of the coming train. Bolivia arrives and pulls him out of the way just in time.
Later, Walter explains that the man's crowns exploded due to the ultrasonic waves. Peter figures that Walternate has agents on this side looking for the missing pieces. Broyles wonders why there would be any pieces on their side. Peter takes the device back to the lab, and Bolivia notes that he has other plans. Broyles thanks Walter for his quick thinking and goes. Walter takes out the safe deposit key.
Later, Walter goes to the bank and opens the box.
At the lab, Peter is examining the device.
Walter goes to see Astrid and shows her the box' contents: shares of stock making him the sole shareholder in Massive Dynamic.
Peter goes over the blueprints of the weapon and contemplates the human trigger in the center of it.
Bolivia goes to the pawn shop and makes her report, informing her superiors that Peter has the first piece and is actively engaged. They respond and tell her to begin work on Dr. Bishop.