Mulder’s family and their roles in the plans for the alien colonization of earth
For many years, Fox Mulder believed that his sister had simply disappeared from her bed one night during their childhood. Only after developing an interest in the X-Files (probably driven by his unconscious recollections) did Mulder undergo regression hypnosis and discover that his memories were actually of Samantha’s abduction by an unseen alien force. Over the years, Mulder’s certainty of what happened to his sister would undergo many revisions and reversals. In the end, however, it seems that the story goes like this:
Because of the demand of the alien colonists, Bill Mulder was required to hand over one member of his family in order to participate in the project. Since he had originally resisted the idea and gave his agreement only at the last moment, Samantha was not present for the gathering at the abandoned hanger where the other families were handed over. Instead, Samantha was taken directly from her home in a combined effort of the aliens and the conspirators (leading to later conflicting memories for Mulder.)
For several years after her abduction, Samantha was not returned to her family as the others were, but kept on a secret government military compound where she was raised by CSM along with his son Jeffrey. There, Samantha kept a diary of all her struggles and the tests that she continue to undergo. (Presumably her use in these tests can acccount for the many clones that have appeared in her image.)
Eventually, Samantha managed to escape from her captors for a time, and she was taken in by the emergency room nurse that treated her. Soon after, however, the government agents tracked her down and came to take her away. When they arrived, however, she had vanished. It seems that she was “rescued” by “walk-ins”, spiritual beings that spare certain children from an impending horrible death (one which would have followed in the hands of her captors) by taking their souls directly. In all respects, therefore, Samantha is dead and Mulder seems to have accepted this fact.
It was in the army that Bill Mulder first met the Cigarette Smoking Man, and the friendship/alliance which they formed would eventually lead him into government work at the most secret levels. Well before the birth of his son, therefore, Bill Mulder was involved in the secret meetings which would bring knowledge of the aliens and their plans to a select group of individuals that would eventually become the Syndicate.
At first, Bill Mulder resisted the idea of cooperation with the colonists, but he eventually gave into the idea as inevitable (still advocating a secret resistance however.) Like the others, Bill Mulder was forced to choose one of his own children to give to the alien colonists in exchange for the right to participate in their plans. Soon after doing so, however, his family fell apart and his wife left him. It was perhaps due to these consequences and the disillusionment that followed that Bill Mulder eventually distanced himself altogether from the Syndicate—“retiring” as it were—and tried to leave behind these events and the secrets surrounding them.
Only after seeming return of his daughter was Bill Mulder forced to face his role in her disappearance and the events related to it. Indeed, these events led him to contact CSM again after many years of silence between them. He was upset to learn of the current status of the project, as well as the subtle threats offered by CSM. This crisis led him to contact his son in order to explain his past and seek his help for the future. Before he could reveal the truth about the plans that were rapidly progressing, however, he was shot and killed in his home by Alex Krycek.
Even as Mulder began to learn of his father’s secret past and his role in the process of alien colonization, he never thought to ask whether his mother had any knowledge of these events or the people involved. Apparently, however, Teena Mulder knew CSM as a friend of her husband from the beginning. Indeed, there are even indications that she had an affair with him early on. (Suggestions that he is actually Mulder’s father have apparently been refuted.)
This closeness put Teena in a position to hear and see many things that, though she couldn’t understand their full implications, probably gave her an idea of the dark undercurrents of her husband’s work. It was perhaps no secret to her, therefore, that her husband’s question of which child was her favorite (a question that she never answered) and the sudden disappearance of her daughter were somehow linked. This led to a resentment towards her husband that tore her family apart, leaving her to raise Mulder with no knowledge his father’s secrets.
The seeming reappearance (and second loss) of her daughter probably started the inner struggle which she would never resolve of whether to reveal her suspicions to her son. On her own, Teena did take some action. She even contacted CSM at one point and had a violent argument that led to a stroke from which she was later healed. (This is perhaps where she received the copy of the investigation of her daughter’s abduction which CSM himself had closed.) Only a few times did she actually give Mulder any hint of what she knew, however. (At one point, she directed him to a hidden alien device which indicates that she knew more about the alien invastion than we think) .
In the end, it seems Teena could not deal with the secrets she carried. After one last failed attempt to communicate her inner demons to her son, Teena burned all her photographs and the secret copy of her daughter’s FBI file. She ended her life (nominally because she had found that she had contracted a fatal form of cancer) apparently still wanting to reveal to Mulder the larger extent of her knowledge.