In Manhattan, New York, a man, George, wakes up at the scene of a crime crash. He runs away into the streets and goes to an apartment. He grabs a resident at his door, chokes him, and shoves him inside. George then wipes the blood off of his face, cracks the bones of his skull repeatedly, and alters his visage. He then reaches into the resident's mouth and attaches a device that alters the intruder's face further. When he's finished, he looks just like the dead man.
Back at the crash site, Junior Agent Jessup investigates and is shown a photograph of the other driver's ID. It belongs to Olivia Dunham.
In Boston, Walter takes Peter shopping for groceries and plans to cook him a custard. Peter insists he doesn't like custard but Walter points out that he loved it as a boy. They're interrupted when they get a call and are summoned to the crash site. Agent Jessup tells them that they don't know what Olivia's status is, and wants to ask a few questions. Peter asks from Charlie, who is en route from Quantico. She tells them that by all signs, there was no one in the SUV when it crashed even though she was apparently in the car. As Walter fiddles with the SUV, it starts momentarily and he quickly gets out. A second after he emerges, Olivia comes shooting through the windshield.
Peter and Walter escort the unconscious Olivia to New York General Hospital. Outside, Broyles meets with Jessup and gives her a report to file that it was an accident and the case is closed. When she balks, he orders her to sign it.
A doctor informs Peter and Walter that Olivia has suffered irreversible brain damage and won't come out of her coma. Walter won't accept it and goes to examine Olivia. He tests for eye response and get nothing, and apologies to her. Later, Peter goes to a bar for a drink and Broyles meets him there. He informs Peter that he's been called to Washington to report and that the government is shutting down the Fringe Division because they've failed to produce useful results. Peter admits they might have a point since they've done nothing but clean up after gruesome deaths. Broyles offers a toast to Olivia and Peter joins in.
At the New York Federal Building, Jessup runs an information search on the Fringe Division but doesn't come up with anything initially. Thanks to a password someone has supplied, she's finally able to access the files and turns up records on a number of deaths that they investigated.
Peter goes back to the hospital and finds Olivia's sister Rachel there. She informs Peter that Olivia had a living will ordering no life support and they're going to shut down her life support in the morning. Peter goes in to it with Olivia and bends over to kiss her as he says goodbye. Olivia wakes up and starts speaking in an alien tongue, and then screams.
The doctor checks Olivia for memory loss and she demands to see Peter. She explains that she went somewhere and someone was trying to stop her. Olivia says that someone told her something she had to do but she can't remember, and she warns that everyone's lives depend on it. She asks Peter to get her gun and warns that she isn't safe.
Peter goes to the Federal Building in Boston and is informed that Broyles is in Washington. When he asks for Charlie, the receptionist doesn't recognize him. When Peter gives her his credentials, she says that they've been revoked. He starts to get violent and Agent Jessup arrives to escort him out. As she drives, she gives him the file and notes that the skid marks at the crash site don't match up. The ones in the back were darker, meaning the driver was speeding up to hit Olivia. Surveillance cameras show the driver, a George Reed, who lives nearby in Lexington. Jessup asks what the Fringe Division is and Peter admits that right now, they don't do anything.
Jessup and Peter break in to Reed's house and find Reed's long-dead body. Peter calls in Walter, who examines the body and asks for it to be returned to his lab. Jessup authorizes Walter's request and Peter wonders why she's helping. She claims that she's just following the case but Peter doesn't believe her.
The shapeshifter, in the form of his newest body, goes to a store and asks for a Selectric 251 typewriter. The store owner insists they never made one but when the shapeshifter insists, the store owner realizes he's one of "them." He hands the shapeshifter a key and directions to the back room. As the shapeshifter goes, the store owner tells him to tell his superiors that he's not waiting around forever. In the backroom is a desk with a Selectric 251. He puts a piece of paper in and starts typing, reporting that the target was terminated in a car crash and a meeting prevented. The shapeshifter requests extraction and then stops typing. The typewriter types on its own, saying that the meeting occurred and the shapeshifter's mission failed. The shapeshifter requests new orders and is told to interrogate the target and then kill her.
Peter and Jessup go to Walter's Harvard lab where Walter is working on the autopsy and preparing for Peter's birthday custard at the same time.
Charlie meets with Olivia. When she insists she's doing fine, Charlie talks about a time when the victim in a domestic disturbance case killed his partner and shot Charlie in the chest. He figures that she has a gun under her pillow, the same way he kept one. Olivia admits that she's so scared she can't even load it.
Walter performs the autopsy and has Astrid start mixing the custard. Inside the victim's mouth he finds three markings on the soft palate. Walter says that the wound made him remember something that does the unthinkable and puts in a video tape. It shows an experiment he and Bell conducted that they did with drugs that augmented the female subject's charkas. The subject talks of the man with the machine and three nails that go in the mouth. She refers to the man as a soldier from somewhere else, another universe. The victim describes how the soldier pushes the machine in the victim's mouth and then changes so he can look like any of them. Peter has Astrid log onto the FBI database to see if any corpse has shown up with three holes in its mouth.
Olivia tries to load her gun without success.
In Washington, a Senate committee interrogates Broyles, who insists that they the country is not secure and that the Fringe Division deals with the unimaginable. They warn that without something to support the fiscal and human cost, they can't maintain the division. Afterward, Broyles meets with Nina Sharp, who warns that the decision is out of their hands. She kisses him and tells him to save the day, the same as he always does.
Jessup and Peter go to the morgue when they get a report of a corpse with similar markings. It's the victim of the shapeshifter's last victim, Lloyd Parr, found two blocks from the crash site. Jessup notes that her father is a soldier and that they stay on mission no matter what. Peter figures that it's going for Olivia.
The shapeshifter goes to the hospital and removes the duplication device from his pocket, then intercepts a nurse.
As Peter and Jessup drive to the hospital, the nurse comes to see Olivia and asks her about her memory. Olivia admits she doesn't remember much. However, she says that she thinks she went to talk to someone and then somehow came back to the accident. The nurse prods her and Olivia says that she can almost remember what she was told. She starts to remember that something was hidden but can't come up with anything further. The shapeshifter then leaps on Olivia and starts choking her.
Charlie meets Jessup and Peter outside and says that only the nurse is allowed in to Olivia's room. They get to the room and Jessup shoots it twice. The shapeshifter leaps out the window, unaffected, and Peter, Charlie, and Jessup go after it. The shapeshifter tries to get behind Charlie near an incinerator but he spins and shoots it at point blank race. Jessup and Peter hear the shots and arrive. The shapeshifter is down and the alteration device is next to it. Charlie says that he's okay.
Later, Peter brings flowers for Olivia and explains what happened. He assures Olivia that Walter will figure out what happened. Peter then repeats the words she said before she woke up but Olivia has no idea what they mean. He explains that it's Greek, and his mother used to say it to him before he went to bad. It means "Be a better man than your father." Peter's mother said it to him after Walter left, and insisted that Peter keep the people that he cares about close. As Peter goes, Olivia asks about the government shutting down the Fringe Division but he insists it won't happen.
Peter meets with Broyles in Washington and gives him the shapeshifter's device as proof he can give to the committee. He insists that they're calling the shots and they're not going to be too late any more. Broyles takes the device and admits that Peter has surprised him.
At home, Jessup is typing up a series of reports referring to the Fringe incidents and tying them into the Bible.
Peter returns to Walter's lab and finds Astrid and Walter ready for him with a surprise party and custard.
Olivia manages to load her gun, and smiles.
Charlie goes back to the incinerator room where he killed the shapeshifter. He takes out the real Charlie's corpse from where he hid it in a laundry bin and dumps it into the incinerator.