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False Family Reunification[]
In 1995, twenty-two years after Samantha's disappearance, a clone of Samantha (who claimed to be her) contacted Samantha's father, William, who then began to gather Samantha's brother and mother at his own home. William Mulder initially announced the news to Samantha's brother, Fox, merely as a "family emergency" and, once Fox Mulder had arrived on William Mulder's porch, William continued to provide vague clues of the issue at hand, noting that Samantha's mother, Teena, needed time and that the occasion was a "difficult time". William Mulder also cryptically stated to Fox Mulder, "The certainty becomes a comfort that allows you to move on. We bury our memories so deep, after all that has been destroyed, never expecting." Moments later, William Mulder announced that the woman, who Fox Mulder could barely see as she talked to his mother inside, was actually his sister.
When Teena Mulder was alone with Fox, she questioned whether the woman was indeed Samantha, to which Fox answered that he could not see who else their visitor might be. The mysterious woman seemed to have Samantha's memories, as she asked her brother (when they later met on the porch) if it was too late to play a game of Stratego and referred to their father as "dad", being of the opinion that he had unable to think of what to say to her. According to the female visitor, she had been nine or ten when she had been returned without any memory, before being placed with a family who had raised her as a daughter. Apparently, she had known that her adoptive parents were not her real family but had forgotten Fox Mulder and his parents. Supposedly, several years prior to her current visit, the woman had begun to experience a troublesome condition that had been diagnosed as "free-floating anxiety" and had been unable to find anything to alleviate or cure the condition, until she had undergone a course of regression hypnosis that had caused her to experience an onslaught of memories concerning abductions and tests she had apparently undergone.
The woman then revealed that the man she referred to as her adoptive father was one of many identical doctors, a group of clones recently encountered by Mulder and Scully while the clones had been avoiding a dangerous Alien Bounty Hunter who intended to hunt and kill each one — (Colony). The mysterious woman alerted Mulder to the reality of the situation — (Colony, End Game). After they discovered that Scully had been kidnapped by the bounty hunter, Mulder questioned his companion why, if she was indeed his sister, she had returned after twenty-two years. She claimed to have explained her reasoning for doing so, but he argued that she hadn't told him enough, influencing her to reveal more about the situation between the clones and the bounty hunter. When Mulder doubted her story moments later, she tried to persuade him to trust her, repeating that she was his sister. He introduced her as such to Assistant Director Walter Skinner, moments after Skinner arrived at Mulder's apartment.
A negotiation with the bounty hunter was arranged in which Mulder would trade the woman for Scully at the Old Memorial Bridge in Bethesda, Maryland. Again referring to the woman as Samantha, Mulder warned her to be careful - when they were alone together, moments prior to the trade taking place - and later called her name after she struggled to free herself from the bounty hunter's grip. The trade did not go according to Mulder's plan, however, and both the woman as well as her captor fell off the bridge, into the icy cold water below. Even though it was unlikely that she had survived, Mulder let Scully know, on the following morning, that he still refused to give up hope of his sister's survival. — (End Game)
Her Return[]
Many of the abductees, including Cassandra Spender and Samantha, were mysteriously returned by the aliens soon after their abduction. Syndicate personnel placed Samantha in the care of the Cigarette Smoking Man at April Air Force Base along with his son, Jeffrey. The Syndicate would perform hybrid tests on her and other abductees in order to create a vaccine to fight the aliens. She kept a diary of these events.
In 1979, after years of abuse and tests at the hands of her "father", Samantha ran away from the Air Force base. She was picked up by Patrolman J. Poole and Detective J. Floyd soon after, and taken to Dominic Savio Memorial Hospital. She was signed in by Nurse Arbutus Ray, who shortly after had a vision of a murdered Samantha. Samantha Mulder was taken, by starlight, from her room that very night. When the Syndicate showed up to take her into custody, she had already gone. — (Closure)
After Her Death[]
In 1989, Fox Mulder was struck with a specialized gas that caused him to see vivid hallucinations. This brought back repressed memories of his sister's abduction. — (Unusual Suspects)
Soon after, he saw Dr. Heitz Werber and went through regression hypnosis to retrieve all of the memories. — (Pilot)
In 1992, one of Fox Mulder's first acts upon being assigned to the X-Files was to open a case on Samantha — (Conduit). Fox believed that if the existence of aliens was proven, then that would invariably confirm his sister's abduction. — (Gethsemane)
On an X-File in 1994, Fox repeatedly saw visions of Samantha while investigating Samuel Hartley for the supposed homicide of Lucy Kelly. Whether this was Hartley psychically placing the image in Fox's head, Fox being slightly delusional, or the ghost of Samantha attempting to contact Fox through Hartley is unknown. — (Miracle Man)
In 1995, one of Samantha's adult clones visited William and Teena Mulder in an attempt to lure Fox into killing an Alien Bounty Hunter. She died trying to kill the Bounty Hunter. Soon after, Fox discovered the colony of Samantha clones in which she was a member, but was unable to destroy the Bounty Hunter. — (Colony, End Game)
In 1996, Fox discovered another colony of Samantha clones, an agrarian workforce, with the help of Jeremiah Smith. These clones were serial ovotypes, or "drones," whose sole purpose was to work. The Samantha clones were not aged past 9 years old. Fox attempted to take one of the drones, but was knocked unconscious by the alien Bounty Hunter, and the Bounty Hunter destroyed the drones. — (Herrenvolk)
Later that year, Fox underwent hypnosis to learn of his past lives. Under hypnosis, Fox believed that during the Holocaust his soul was in the body of a Jewish woman. He believed that Samantha's soul was in the body of the Jewish woman's son. — (The Field Where I Died)
During an investigation into the murders of John Lee Roche, Fox began to believe that it was Roche, and not aliens who had abducted his sister, and that Roche had killed her. Despite the fact that Roche had visited the Mulder home before, Fox found that Samantha was not one of Roche's victims. — (Paper Hearts)
In 1997, the Cigarette Smoking Man brought a woman, possibly another clone of Samantha's, to meet with Fox Mulder. The woman claimed that she was Samantha, and told Fox that she didn't want to be reunited with their mother. She left, never to contact Fox again. — (Redux II)
In 1999, while undergoing hybridization tests, Fox imagined that the Cigarette Smoking Man was Samantha's father and she lived a block away in a perfect suburban neighborhood. — (The Sixth Extinction II: Amor Fati)
In 2000, Teena Mulder committed suicide. This occurred while Fox was investigating the disappearance of Amber Lynn LaPierre. Over the course of his investigation, he was told by Kathy Lee Tencate that his sister was a "walk-in". — (Sein Und Zeit)
Fox once again began investigating his sister's disappearance. With the help of Harold Piller, Fox discovered the events of 1979 and his sister's apparent death at Dominic Savio Memorial Hospital. — (Closure)
In 2008, Fox Mulder kept a photo of his beloved sister in his office while working on his own personal projects. — (The X-Files: I Want to Believe)