Doggett continues to investigate Kersh, despite opposition from Skinner, who wants to protect Scully and the baby. Mulder disappears. Shannon McMahon [Lucy Lawless], who has strange underwater powers, is drowning people connected to a polluted water cover-up. A rotating mobile over the crib makes Scully worried about her baby, so she rejoins the team. She does an unauthorised autopsy of one of the drowned men for Reyes, but the body disappears before the FBI can make a case against them. Skinner and Doggett then investigate what the drowned men were up to. McMahon drags Doggett deep underwater...
The investigation continues. Lots of people keep changing sides, for no very readily apparent reason. Shannon McMahon claims to be a prototype super-soldier. A ship being used in the super-soldier research is discovered, then scuttled, destroying all the evidence. Shannon McMahon is apparently killed, or maybe not. Doggett gets to keep his X-Files job.
Scully starts teaching forensics at the FBI academy. Some strange killings look like satanic rituals, but Doggett suspects a psychopathic professor in a mental institution is manipulating them all.
On a stakeout, Reyes is killed and Doggett is shot and critically injured. Then Skinner calls a still-alive Reyes to tell her about Doggett, but she insists she was with him at the time. They discover Doggett was shot with Reyes' gun, but that it hasn't been fired. Reyes suspects the real killer may be from a parallel dimension, and that the two Doggetts have swapped worlds. In a stakeout, the killer nearly gets her, but is killed first. Reyes switches off the other Doggett's life support, and the real Doggett is returned. [A good plot, ruined by a ridiculous "rewind" ending.]
The agents investigate when a teenager's brain is apparently eaten by insects during a "dumb-ass" TV stunt. There's a nerdy loner nearby...
Doggett tells Scully that someone wants to contact Mulder to give him information about the super soldiers. Doggett is upset that Scully won't trust him about this information. Then he gets more upset when Scully goes to meet the contact, and agrees to set up a meeting with Mulder. But it is a trap: the agent is a super soldier. Who appears to be surprisingly vulnerable to iron ore.
Doggett wakes up in a small Mexican town, amnesiac. He gradually learns he is one of the disappeared: people the drug Cartel who own the town don't want around. The only memory he has are visions of his son. Reyes tracks him down, and he gets his memory back.
Reyes feels compelled to investigate when murder victims are being skinned alive. There are strange parallels with a case from 1960, and then even earlier cases. The victims seem to be reincarnations of some earlier murderers, being punished for their crimes, and Reyes the reincarnation of the detective who consistently fails to solve the case.
A UFO cult find a spaceship with religious etchings in Canada, but the FBI insist it isn't an X-file. A deep-cover FBI agent tries to kill Scully's baby. She shoots him, and discovers a piece of spaceship in his jacket pocket, which is strangely attracted to the baby. Skinner tells her the agent had said that Mulder is dead. Scully gives William to the Lone Gunmen to hide. But a cultist kidnaps him, putting Doggett into a coma.
The hospitalised FBI-man asks for the piece of spaceship, which heals him. He tells Scully the cult want to save William, because he's prophesied to lead an alien race of super-soldiers to rule the Earth, provided Mulder is dead. The agent tried to kill him to stop the prophesy. Someone with a bumpy back of their neck kills the agent. The cultists say Scully can see her son if she brings them the head of Fox Mulder, who isn't as dead as they had believed. She trails them back to their lair. William seems to cause the spaceship to take off, incinerating all the cultists, and leaving him lying in a crater for Scully to find.
A car accident leaves Agent Reyes apparently brain dead. But Doggett refuses to give up hope. Reyes is awake in a strangely deserted hospital floating in nothingness, with just two other patients. Audrey, the flower delivery woman from the hospital can travel to this other world. Reyes gives her a message for Doggett. He starts investigating. The same doctor is treating all three patients, and is killing them. Audrey tells Reyes she has to give the world a sign. The doctor discovers Audrey, and kills her. Reyes wakes up.
A serial killer originally arrested by Doggett is released after 13 years, after DNA evidence shows he's innocent. A strange bearded man keeps killing people. The prisoner is in fact this other man, too. Doggett refuses to believe the evidence of his own eyes when he shoots the bearded killer, and the unbearded prisoner's body is recovered.
Reyes is convinced the victims of a serial killer are linked to numerology. Scully discovers a 666-ring bruise on each of the victims. Whilst investigating, Reyes and Scully get trapped in an underground car park along with a mysterious man [Burt Reynolds], who encourages Reyes to follow her ideas. She realises the killer is hiding there too. Doggett sees the shape "9" in the killer's route, and arrives in time to rescue Reyes, and shoot the murderer. The mysterious man disappears.
The agent from accounting who helped Doggett previously [ 8.19 Alone ] . A young boy's grandmother says he insists that monsters killed his mother. The boy's father has taken him to a remote house in Philadelphia. The agent, Doggett and Reyes investigate, and end up trapped in the house. Scully investigates the death of the boy's cat, and decides there is a problem. The boy is drawing horrific pictures from his imagination, that then come true. But they don't work on Doggett, because he doesn't really believe they can. [So how did they work on the cat?] Doggett in turn convinces the boy his is being burned. The boy ends up in a psychiatric hospital where they are dulling his imagination -- by giving him TV.
A scam artist claims to know about one of the Super Soldiers. He says it is Eve -- a past associate of the Lone Gunmen [from the short run spin-off show?]. Doggett and Reyes enlist the Lone Gunmen's help, and they discover Eve has murdered a shark researcher. When they find her, she explains she is trying to foil her father's terrorist plot to spread a deadly virus embedded in a shark cartilage capsule in two carriers. They find the second carrier with only seconds to spare, and the Gunmen sacrifice their own lives to stop him.
Doggett captures an intruder in the X-files office, who is very badly scarred. He claims to have been the victim of an alien experiment, and to have been sent by Mulder to get certain files. Scully has these files in her apartment. Doggett believes the man actually is Mulder, and DNA evidence bears this out, but Scully is not convinced. It's all a ruse to bet close to baby William, and the man injects the baby with some inknown compound. He claims it is to stop William becoming the alien ruler he was designed to be -- and he turns out to be Cigarette Smoking Man's other son -- Mulder's brother. William is apparently unharmed by the injection; nevertheless Scully decides she can no longer keep him safe, and gives him up for adoption.
A strange FBI cadet is brilliantly good at explaining deaths. Then he says he has some new information about Doggett's son's murder. His information leads Doggett to a New York petty gangster. Reyes' ex, the FBI Assistant Director, gets him access to the relevant case files. Then Reyes realises the guy is someone she saw giving the AD money in New York three years ago. When they confront him, however, the AD says that was an FBI operation, and that the cadet is actually an imposter, a schizophrenic from a psychiatric hospital. But the AD was being bribed by the gangster, and when he realises the man was the boy's killer, shoots him, just before Doggett can. Doggett has closure on the case at last.
Two men who claim a house is the interior set of The Brady Bunch end up dead with their heads beaten in. The team discover a powerful telekinetic, who can make things happen at will. He summons the perfect Brady family for company, and had forcibly ejected the intruders from his house. He agrees to come back to Washington to be studied. It looks like the X-Files team will finally get proof of a parapsychological phenomenon. But then he gets sick -- using his powers is killing him. So they tell him not to use them any more.
Mulder breaks in to a military establishment to discover some data,
and "kills" a super-soldier. He is put on trial in a secret
court for murder. He chooses Skinner as his defence lawyer, but the
trial is rigged, and he is sentenced to death. Skinner and Doggett
break him out, and he and Scully go to New Mexico to find a wise man.
It turns out to be Cigarette Smoking Man. We discover the date of the
alien invasion is set for 22 December 2016. And after 9 years of
patient viewing, we are treated to some final religious mumbo-jumbo.