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This episode takes you behind the scenes into the production room to show you character discussions, the many goofs made when shooting episodes, and more.
Basically the same thing as "Secrets to the X-Files", the episode shows the past highlights including Scully's abduction and Mulder's sister, and new ones from Season 3. There's a brief segment of clips from Season 3.
This episode shows various clips from previous episodes (up to "Our Town"), explains the history of Mulder and Scully including how/before they met, then explains the other important characters (like Skinner, X, Deep Throat, CSM) and then summarizes/explains highlights (like Scully's abduction and the alien clones).
When an unexpected person comes to Mulder's rescue, Mulder refuses to slip north over the border to safety. Instead, he heads southwest to the Anasazi ruins of New Mexico seeking a mysterious wise man whom the Indians call The Keeper of the Truth.
After not knowing Fox Mulder's whereabouts for the last year, A.D. Skinner and Agent Scully learn he's being held for the murder of a military man he couldn't possibly have killed: Knowle Rohrer, one of the government's secret super-soldiers. With Skinner acting as Mulder's defence, people who Mulder has dealt with during his last nine years as an FBI agent testify on his behalf. But the military tribunal isn't interested in the truth.
Doggett and Reyes investigate a murder outside the house that the original Brady Bunch series was filmed in. The house is owned by a man named Oliver who is obsessed with the show and has rigged the house into a series of traps and changing appearances to look like the Brady house.
When an FBI cadet with amazing profiling skills approaches Doggett, Reyes and Scully with a lead on a suspect in a series of recent murders, he claims the same killer is responsible for the death of Doggett's son. The agents find themselves wondering if his knowledge of the deaths is because of his obsession with the cases he has studied at Quantico or if he is in some way involved in the murders.
Doggett catches someone in the X-files office trying to steal documents pertaining to Mulder's sister. The intruder is a severely scarred man who blames his disfigurement on Government conspirators. He claims the source of that information - and, in fact, the one who helped him gain entry - is Mulder. Although he refuses to divulge the missing agent's whereabouts, the mystery man has enough knowledge of the X-files and its history to lead Doggett to suspect that he just might be Mulder himself. Scully's fears for the safety of her son are elevated when he is injected with an unknown substance. With the mystery surrounding William becoming even more darker, Scully must allow herself to send him away for his own safety.
When Morris Fletcher approaches agents Doggett and Reyes with information related to "Super Soldiers", they turn to the Lone Gunmen. The Gunmen, however, are knee-deep in a bio-terrorist's plot to release a deadly toxin into the population but the Gunmen find that they may have to make the ultimate sacrifice for their cause.
Monsters hiding under a little boy's bed may be more than just the product of a vivid imagination when agents Harrison, Doggett and Reyes investigate. They find out that there is more to the story of the mysterious death of the child’s mother who apparently stabbed herself repeatedly. Meanwhile Scully conducts an autopsy on a dead cat.
When Reyes uses numerology to connect the murders of several women to an obsessed serial killer, she and Scully become trapped with a mysterious checker-playing man who may or may not be the killer. The question then becomes who is going to be the next victim.
Scully, Doggett and Reyes investigate an old case that Doggett worked on as a cop in Brooklyn, dubbed "The Screwdriver Killer". They try to determine whether the man who was convicted and has just been released from prison was actually the man responsible for the murders.
Doggett and Scully look for answers that will save Reyes' life after she is injured in a horrible car accident. Yet Reyes is also fighting to stay alive in the netherworld between life and death. But before long Reyes realises that she may have little time left when others in the netherworld start to disappear.
Scully is anxious to recover William from his kidnappers and takes matters into her own hands when the FBI's attempts to assist in the investigation are less than helpful. With the help of the Lone Gunmen, Scully discovers terrifying information about her child's captors, and is once again forced to confront the mystery regarding the sinister interest in her son.
When pieces of the spaceship beached in Africa resurface, the conspiracy within the FBI attempts to hide the information from the X-Files, especially the one person for whom the pieces have a special significance - Scully. When Doggett and Reyes discover that Scully and her child have been put in great danger, they race to protect her and William from the evil forces pursuing him, and Scully is forced to take drastic measures to protect her child.
Agent Reyes takes the lead while investigating an X-file case, surrounding a man found skinned alive after having visions of seeing other people appearing skinned alive. Reyes calls on Scully's expertise to help on the investigation.
Scully and Reyes join forces to try and find Doggett when he goes missing. Doggett has his own problems, having woken up in jail in Mexico suffering from amnesia. With no knowledge of who he is, Doggett is befriended by a local who soon has him working smuggling illegal immigrants across the border.
Scully is approached by a couple who claim their baby has the same abilities as William and have information about the super soldier program, however they will only talk to Mulder, believing him the only person who can make the connections and uncover the truth. Scully is forced into an awkward situation when she has to decide whether to put Mulder's life in more danger even though she desperately wants to see him.
When a stunt on a local cable reality show goes horribly wrong resulting in a man's death, Doggett and Reyes investigate. But when flies pour out of the victims eye sockets, they find themselves relying on Scully's expertise and they ask her to join the investigation.
During a stakeout of murderer Irwin Lukesh, Doggett sees Reyes attacked by Lukesh but then we see Reyes and Doggett in her apartment, apparently both fine. Elsewhere at the same time, Doggett is shot and Lukesh identifies Reyes as the shooter. While Reyes is asked for her badge and gun by AD Follmer and Doggett lies in hospital near death, the conflicting circumstances of the stakeout and Doggett's shooting do not add up and it becomes clear that Lukesh possesses the power to switch between parallel universes and alter the events in each.
Doggett and Reyes investigate the murder of a couple in West Virginia that has all the signs of a satanic ritual killing. They link the murder to a doctor incarcerated in a mental institute and Doggett becomes convinced that the doctor is orchestrating the crimes from within the hospital.
Doggett catches up with Shannon McMahon, the woman who the EPA official picked up. She claims to be a super solider and that the people she has killed were preparing the water supply and she wants Doggett to expose the truth.
Agent Doggett investigates the death of an EPA official after his car is forced off a bridge by a woman he picked up. He asks for assistance on the case from Scully, who has returned to her teaching position at the FBI Academy in Quantico.
