Walter wants to make Peter custard for his birthday because it was his favorite as a boy, but Peter explains that he has never liked custards. Walter says he merely cannot remember. They get a call about an accident in Manhattan.
Olivia's car is at the scene of a car crash, but she's nowhere to be found. Attending to the accident is FBI Agent Jessup. Walter senses something is awry, when suddenly Olivia flies through the windshield as if she appeared out of thin air. With her terrible injuries, Walter and Peter expect the worst. Broyles lets Peter know that the Fringe division has been shut down.
Olivia abruptly awakens in the hospital and says a phrase in Greek to Peter. She has no memory of what has happened to her. Olivia confides in Peter that "He" told her something but she doesn't know who "He" is. "I can't remember but there's something that I have to do," she says cryptically in fear. Olivia begs him for a gun.
Agent Jessup finds surveillance camera photos from the time of the accident. Yet the man in the car who was chasing Olivia is already dead in his home. His body has expelled all of its excess water. Walter takes the body back to his lab and discovers marks in its mouth. He shows the team a video of an experiment that he and William Bell conducted in the 1970s where they gave massive amounts of hallucinogens to a young woman. In her altered state, the woman described a shape shifter who used a device that was pronged into victims' mouths.
The shape shifter who has assumed the dead man's body goes to an antique office equipment store in the Bronx and is granted entry to a secret back room with an old typewriter on a desk with a mirror. He puts in a sheet of paper and types that he has exterminated the target. The reflection in a mirror mysteriously types back the message that the target is still alive. It instructs the shape shifter to interrogate the target and kill her.
The shape shifter takes over the body of a nurse in the hospital and then tries to get Olivia to divulge what she remembers. The shape shifter in the guise of the nurse attempts to kill Olivia with the device, but Agent Jessup arrives in time to save her. The shape shifter escapes out the window. As the agents chase her, they hear a shot. They find Charlie standing over the body of the nurse.
Thinking they are now all safe, Peter tells Olivia that the Greek phrase she said to him earlier was something that his mother used to repeat about protecting those close to you. Peter then meets with Broyles and hands him the broken device found on the shape shifter. "We're calling the shots now," Peter says. With this evidence, the Fringe division is reopened.
Unbeknownst to anyone else, Charlie is dead. The shape shifter who has taken his form disposes of the real Charlie's body. What appears to be Charlie is now after Olivia.