A man who can affect the magnetic field around him causes an elevator malfunction which kills a lot of people. Dr. Bishop surmises that some modified carrier pigeon could lead them to the man. It turns out that a vicious scientist has been experimenting on this magnetic man. With the pigeon's help, Olivia and Peter find out their location and arrest them. 

An eyebrowless bald man known as the Observer is noticed by Agent Dunham because he was present at every mysterious scene. A cylinder emerging out of the ground causes casualty in NYC, and Dr. Bishop is recruited to shed light on the mystery, but he steals the cylinder to return favor to the Observer for saving his life. Another man is looking the cylinder, and he interrogates Peter, ultimately finds where Walter has hidden it. At last, it disappears again.

Roy has been seeing terrible scenes in his head, including a bus attack with mysterious gas weapon. Walter is recruited to investigate the accident, and he recalls experimenting on a subject allowing messages to be sent into people's head. While performing a surgery on Roy's brain, Walter alters his brain to receive voices instead of images, and the information he received helps Agent Dunham to track down the culprit of the bus attack.

A woman dies after giving birth to a bizarre baby who ages rapidly and dies four hours later. This reminds Walter of a project he researched with his colleague Dr. Penrose. It reveals that Dr. Penrose has made a major breakthrough; he created a subject,having it to kill prostitutes to cut out their pituitary gland, so he can complete his project. Agent Dunham finds out the crime scene, and Peter saves a girl, but Dr. Penrose escapes.

An airplane lands at Logan Airport in Boston. All of its passengers die from an unknown virus, which causes their skin to melt down. Phillip Broyles leads several federal agencies to investigate the accident; he orders Agent Olivia Dunham to examine a storage facility, where John Scott, who has a romantic relationship with Olivia, is infected with the virus when chasing a suspect. 

To save John's life, Olivia enlists the help of Dr. Walter Bishop, a scientist versed in fringe science who has been incarcerated in a loony bin for 17 years. Walter invents a system, which enables Olivia to communicate with a comatose John. After identifying the suspect, Olivia raids his apartment, arresting him. John is saved, and Olivia finds out that he is working with the criminal. In a car chasing, John's car turns over, and he dies.