X-Files Season Nine

Nothing Important Happened Today
Doggett's investigation of Kersh and the FBI isn't making him any friends, especially Brad Follmer, a new Assistant Director who has a romantic past with Reyes. Meanwhile Scully denies to tell anyone where Mulder has gone while a female super soldier is on the loose and may give Doggett the clues he needs to make his point known. 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.
Nothing Important Happened Today II
While Reyes and Skinner try to convince him otherwise, Doggett practically goes rogue for his own pursuit of the Truth. His findings, and help from the female super soldier Shannon McMahon, may lead to answers critical to the status and health of William Scully. But Knowle Rohrer is back from 'the dead' and stands in their way. 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.
Dæmonicus
A professor/inmate in a psychiatric ward may be influencing other men to kill ritualistically. Though Doggett sees it as pure manipulation, Reyes can't help but suspect none else but the devil himself possessing the professor's body. 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.
4-D
A killer murders Reyes and mortally wounds Doggett...in another dimension. Reyes, under investigation for a nearly killed Doggett realizes the killer can shift dimensions to fill out his disgusting fantasies. 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.

Lord of the Flies
Doggett and Reyes are unsure whether a boy intentionally or unintentionally can control the habits of flies; during the investigation Scully acquires a new 'partner'. 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.
Trust No 1
Mulder contacts Scully which sets off a chain of events involving an NSA man obsessed with speaking and giving information to Mulder. 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.
John Doe
Doggett wakes up in Mexico and can't remember his name or what he is doing there. His only clues are small flashbacks of a child (his son) and two mysterious marks on his head. 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.
Hellbound
Reyes finds herself inexplicably connected to a case involving ex-cons who are being skinned. 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.
Provenance
A man is chased from the Canada/US border and reportedly burned alive though his body is not found. Meanwhile, in the burned remains the FBI finds papers with the same UFO markings Scully found in Africa. 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.
Providence
Scully's baby becomes a bargaining chip for a psychotic UFO cult that feels the baby is ultimately connected to a UFO they have uncovered. 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.

Audrey Pauley
Reyes is seriously injured in a car accident and finds herself in a hospital similar to purgatory with other hospital patients suffering from serious traumas. Slowly they all begin to disappear. Meanwhile, in the real world, Doggett refuses to accept his friend's 'mortal' wounds and uses a bizarre hospital employee to both connect with Reyes in the other-world and capture a 'Dr. Death.'
Underneath
After thirteen years in prison, a man named Fassl is released and cleared of murder charges when DNA evidence proves he had nothing to do with the murder of an entire family though he was present on the scene. Doggett, who made the arrest, refuses to accept Fassl's innocence and pursues the case again. 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.
Improbable
Reyes, Doggett, and Scully are pulled into a bizarre serial murder case involving the number '3', numerology on a whole, and an eccentric man who likes to play checkers. 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.
Scary Monsters
Reyes and Doggett, with the aid of a young Mulder-worshiping FBI agent, investigate a father who is exhibiting bizarre behavior regarding his son who he has kept hidden from the outside world. 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.
Jump the Shark
The Lone Gunmen, with the (unwanted) aide of Morris Fletcher, must stop a destructive virus from entering the populace. 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.

William
A disfigured man attacks Doggett trying to retrieve X-Files for Mulder...but he might be Mulder himself. 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.
Release
A Frank Black-esque cadet in Scully's class directs Doggett to a current murder case that may have something to do with a case that went unsolved 9 years prior...the murder of his young son. 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.
Sunshine Days
Reyes and Doggett investigate two murders revolving around a house that is, at some points in time, identical to the Brady Bunch house. 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.

The Truth
Doggett and Skinner help Mulder escape his military prison after he is found guilty of murdering the super soldier Knowle Rohrer. Mulder then takes Scully with him to find out once and for all what "The Truth" is and if his working on the X-Files for the previous nine years was worth anything. 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. 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.
Secrets of the X-Files
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).
More Secrets of the X-Files
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.
Inside The X-Files
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.