With his mother on deathbed and the alien bounty hunter in pursuit, Mulder decides to put the alien healer in mortal danger for a chance to finally uncover the whole truth behind the alien conspiracy. Meanwhile, Mr. X's cover is blown.
Agents Mulder and Scully investigate a doomsday religious cult, which inadvertently draws Mulder into recalling a past life and how Scully and others were there with him in the field where he died during the American Civil War.
The Lone Gunmen reveal the (possibly fake) secret history of the Smoking Man to Mulder with focus on three episodes from his life - the assassination of JFK, his attempts at becoming a novelist and one of his UFO cover ups.
A tip from Krycek takes Mulder to a gulag in Tunguska, Russia where prisoners are being used for experiments with the black oil alien virus. Meanwhile, Scully's colleague is infected with the same virus which lay dormant in a meteorite.
Mulder tries to stop a Russian supersoldier from destroying the site in North America where the black oil virus can be excavated. Scully is jailed after she refuses to reveal Mulder's whereabouts at a Senate subcommittee hearing.
Desperate illegal immigrant dubbed El Chupacabra who can't speak any English becomes patient zero for a possibly alien infection and goes on the run from INS, the FBI and his own brother who blames him for the death of his girlfriend.
A headless corpse of a paramedic walks out of the hospital morgue triggering a manhunt for a man with unimaginable regenerative powers, that come at a terrible cost. The case makes Scully realize in shock that she may not be well.
Mulder takes a vacation to visit Graceland while sending disaffected Scully to Philadelphia to look into Russians with ties to UFOs. She becomes attracted to a secretly unstable young divorcee whose tattoo is telling him to kill women.
An embittered Vietnam War veteran who can apparently somehow make himself invisible to everyone around him is murdering military officials. In order to attempt to stop him, Mulder and Scully must first uncover his motives.
While investigating the unexplained crash of a commercial airliner the agents' search for answers leads to the bottom of a desolate lake and a startling discovery involving Mulder's alien abductee friend Max Fenig.
Mulder and Scully continue their investigation into what really caused the airliner to crash, as the military insidiously begins to cover up the truth and even tries to murder the agents. Someone close to Scully is killed in the process.
Apparitions of women killed by a serial killer start appearing to people. Mulder figures they may be harbingers of death for those who see them. Scully is skeptical until she sees one. Their only lead is an autistic psychiatric patient.