With the X-Files shut down, Mulder travels to Puerto Rico on a tip from his mentor in the Senate to uncover the reason behind the sudden reactivation of a remote long abandoned SETI-like communications station.
Mulder is on the manhunt for a Vietnam veteran who can project his consciousness into other people's minds to kill them. Mulder and Agent Krycek try to uncover the conspiracy behind the killer's powers.
While Agent Scully is still missing, Agent Mulder embarks upon an investigation involving vampires in Los Angeles, subsequently becoming involved with a sultry female vampire who yearns to escape her lifestyle.
Scully's comatose body is discovered at a local hospital and her life is hanging in the balance. When Mr. X shows Mulder the high price he'd have to pay if he truly wants justice for Scully, Mulder must choose between hope and revenge.
At a remote outpost, scientists watch as their camera picks up a moving shadow on the inside of a smoldering hot volcano, too hot for any living creature to survive. Mulder and Scully arrive and notice that everyone is acting strangely.
A vegan religious cult is accused of kidnapping local teenagers for some type of ritual. Mulder and Scully begin to suspect that a different kind of conspiracy is at play when Scully sees Deep Throat's killer in town.
A pregnant police woman experiences visions that lead her to the remains of two FBI agents who went missing in the 1940s while on the trail of a serial killer that later got caught. The killings begin again but the only suspect is now 77.
When someone sends Mulder and Scully obituaries showing three separate but identical men apparently having died, the agents investigate, but things take an unexpected turn when Mulder receives a call from his father.
In a small town in Idaho, a man is killed by what seems to be an invisible elephant. Mulder's investigation into the local zoo, its owners and a local animal rights group uncovers evidence of insidious alien experiments.
The crew of a U.S. military ship that disappeared in the Norwegian Sea is found dead from what seems to be rapid aging. Thinking it's another Philadelphia Experiment, Mulder boards the ghost ship along with Scully and a local skipper.
Scully's former student, Det. Kelly Ryan, asks the agents to help her catch a runaway government scientist responsible for several mysterious disappearances. Mulder realizes that the man is deathly afraid of his shadow for some reason.
Reports of foxfire on a field in Dudley, Arkansas lead Mulder and Scully to a bizarre situation regarding the townsfolk. Employees of the Chaco Chicken Corporation are displaying bizarre behavior, and the death rate is slowly increasing.
Mulder receives an encrypted computer disk containing the defense department's top secret files on extraterrestrial life and becomes a target. Scully takes him to a Navajo family that unearthed a buried secret to decipher the disk.