John Scott (Mark Valley) was Olivia Dunham's (Anna Torv) partner in the FBI, and her lover. While investigating the case of Flight 627, John became exposed to the contagion that had infected and killed the flight's passengers, and he was put into a drug-induced coma in an attempt to slow the illness.
In order to find answers about what or who caused the contagion to be released, Dr. Bishop (John Noble) and the Fringe Division used a process called synaptic transfer to connect Olivia's mind to John's. Through this process, John was able to share his memories with Olivia and show her the face of the perpetrator.
Eventually, Olivia was able to find the man who created the contagion, and Dr. Bishop in turn created a cure for John. However, when John was cured, it was revealed that he was secretly working for the NSA in order to infiltrate a bio-terrorist group that was dealing in weapons.
When Olivia tried to confront him, they got involved in a car chase, which ended up being fatal for John. Later in the season, it would be discovered that John was on the Original Fringe Team and had kept a secret file system of all of their cases.
"Ask yourself why … why Broyles sent you to the storage facility."
"You do that and we will come after you -- I will come after you."