Season two follows the continuation of a war between two universes, the prime and the parallel, exploring the ever-blurring line between science fiction and reality, where hybrid monsters tear through sewers, thieves walk through walls, and portals open to worlds unknown.
An amnesiac Olivia makes her return from the parallel universe, while Walter, Pete, and Junior Agent Amy Jessup investigate the mysterious death of a man found with puncture holes in his palate. Meanwhile, Broyles defends the Fringe Division from a Senate subcommittee threatening to shut the organization down.
A highway construction worker is the seventh in a series of mysterious disappearances in Lansdale, PA. The team come to investigate and finds traces of a mysterious paralytic. Meanwhile, Walter tries to send frogs to an alternate reality and Olivia realizes her recent trip has altered her in ways she can barely understand.
When an American officer who served in Iraq blows up in a Philadelphia train station, the Fringe Division investigates and determines that something turned the man into a living bomb. Peter and Olivia travel to Iraq to determine if Peter's contacts can shed some light on the situation.
Olivia begins to regain her memories of her encounter with William Bell. Meanwhile, the "First Wave" tries to collect the head of their leader, and the traitor makes his move.
A man in Seattle goes berserk, attacking his boss and claiming his victim is a demon. After the killer dies of what appears to be exhaustion, the Fringe Division discover it's only the first in a series of killings where the persons initiating the attacks were in a dreaming state while awake
Human beings are reduced to ash statues and Broyles realizes that the same person responsible murdered five other persons four years ago... a case that he never solved.
Two men kidnap a teenage boy using mind control abilities. The boy's father works for Massive Dynamic but Nina insists that the company hasn't been developing mind control, and has no idea who the two kidnappers are. The truth or falsehood of her statements are soon confirmed when Peter encounters the person responsible for the boy's abduction.
The Observer chooses to do something other than observe, abducting a college student. However, when the Fringe team investigates, they discover that there is more than one Observer.. in both time and space.
A Chinese Triad is using illegal aliens to breed parasitic worms that eventually kill their hosts. When a ship runs aground, Fringe Division learns of the operation and tries to locate a second ship before the passengers on it suffer a slow, agonizing death.
The First Wave breaks into a mental hospital and cures a long-term patient suffering from schizophrenia. When the Fringe team investigates, Olivia discovers that the group's leader has one of the heads stolen from cryogenic storage months earlier. Meanwhile, two other mental patients are cured of their schizophrenia and the team soon realize that something was taken from each patients' brain... and Walter holds the key to realizing what First Wave is after.
A teenage girl pronounced brain dead wakes up in the middle of the operation to remove her organs... speaking numbers in Russian. When the Navy confirms that the numbers are nuclear launch codes and a missing officer named Rusk knows them, the search is on for the missing man.
A state trooper picks up a runaway boy, but when he undergoes a strange transformation, three murders result. The Fringe team is called in to investigate and discover that a small town harbors a horrible secret.
A Dutch industrial consultant arrives for an appointment and dies in a painful explosion of blood. Olivia and Peter arrive on the scene first and discover that the blood contains a pathogen and everyone in the building may be contaminated. While Walter and Astrid work outside the quarantined building to create a cure, the virus develops unique characteristics that pose a danger to the entire world.
When all of the groom's relatives asphyxiate at a wedding, the Fringe division investigates and quickly ascertain that a human agency is responsible. Walter realizes that the formula for the toxin was based on research conducted by his father, Robert Bischoff, and that the killer isn't stopping with a single test of his lethal concoction.
The arrival of a building from the alternate Earth causes massive death and destruction to those occupying the site at its arrival. Walter soon realizes that to equalize the balance between universes, another building will have to disappear... along with everyone inside it. The team's only chance is for Walter to activate Olivia's long-buried ability to distinguish objects from the other universe.
A healthy woman dies of rapid-onset cancer in a matter of minutes, and the Fringe team is called in to investigate. The killer has connections to Jacksonville... and Olivia is a potential victim. Meanwhile, Olivia tries to come to terms with her knowledge of Peter's origins.
When the passengers on a commuter train all die instantly of massive power loss, the team realizes that a time traveler is responsible... and that it may be impossible to apprehend him. Meanwhile, Walter writes a letter to Peter explaining his origins.
Two teenagers turn up dead and evidence indicates that shapeshifters have borrowed their forms for some special mission. While the Fringe team tries to track them down, Peter grows increasingly suspicious of Walter's secretive behavior.
When Peter disappears, Walter seeks solace in marijuana. In that state of mind, he and Astrid babysit Olivia's niece Ella, and Walter tells her a fairy tale of a gentle inventor, a stolen glass heart, a detective looking for true love, and a mysterious group of bald men known as the Watchers.
In Noyo County, Washington, Peter stumbles across a grisly murder with ties to Newton and First Wave. He is forced to team up with a suspicious sheriff to get to the heart of the case. Meanwhile, Walter has trouble functioning without Peter, and worries he will be sent back to the mental institute.
When Walter discovers that Peter has traveled to the alternate universe, he and Olivia gather three cortexiphan children with the ability to transition safely between the two Earths.
Walternate asks Peter to help complete the device, while the fugitives Walter and Olivia are reunited with William Bell. Meanwhile, the alternate world's Fringe Division closes in on the invaders, and Peter must make a life-shattering decision.