Fringe follows the casework of the Fringe Division, a Joint Federal Task Force supported primarily by the Federal Bureau of Investigation, which includes Agent Olivia Dunham; Dr. Walter Bishop, the archetypal mad scientist; and Peter Bishop, Walter's estranged son and jack-of-all-trades. They are supported by Phillip Broyles (Lance Reddick), the force's director, and Agent Astrid Farnsworth (Jasika Nicole), who assists Walter in laboratory research. The Fringe Division investigates cases relating to fringe science, ranging from transhumanist experiments gone wrong to the prospect of a destructive technological singularity to a possible collision of two parallel universes. The Fringe Division's work often intersects with advanced biotechnology developed by a company called Massive Dynamic, founded by Walter's former partner, Dr. William Bell (Leonard Nimoy), and run by their common friend, Nina Sharp (Blair Brown). The team is also watched silently by a group of bald, pale white men who are called "Observers".

Season 1 introduces the Fringe Division as they investigate cases that form "the Pattern" geographically centered around Reiden Lake in New York state, many of which are orchestrated by an international network of rogue scientists known as ZFT (Zerstörung durch Fortschritte der Technologie, or in English, Destruction through Advancement of Technology), led by David Robert Jones (Jared Harris), who are preparing for a doomsday event. The ZFT threat appears to end when Peter kills Jones as he attempts travel to a parallel universe.Olivia comes to learn she was a child test subject for Walter years ago (then known as Olive) for a nootropic drug, Cortexiphan, giving her weak psionic abilities. Walter also struggles with adjusting to normal life in Peter's care after living seventeen years in a mental institution while hiding the fact that Peter is from the parallel universe, "his" Peter having died as a child.