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This is just one of the many things I was confused about after watching all episodes of The X-Files in a marathon.

First, it seemed to be hinted that her father allowed her to be taken by aliens as part of the conspiracy. This seems to be supported by what we see in flashbacks and the Samantha clones in the first movie.

In Season 4 the episode Paper Hearts seemed to imply that Samantha had been killed by a child serial killer.

In Season 7 it is implied that Samantha was taken by a type of Supernatural entity to a better place and is dead in our world.

These explanations seem to contradict one another to me. Is there a good in universe explanation for what happened to Samantha Mulder?

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    Wasn't there an episode where the Smoking Man showed Agent Mulder his sister at some hotel or something? Also – Dylan Yaga Mar 7 '12 at 16:12
  • I seem to recall that on cracked.com they stated this was a screwup by show creators and never addressed for real – DVK-on-Ahch-To Mar 7 '12 at 16:56
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    I seem to recall the one at the hotel ended up being a clone. But it's been a long time since I watched. – BBlake Mar 8 '12 at 18:46
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My understanding is that the explanation of Samantha Mulder's fate given in the 7th season episode "Closure" was definitive.

She was part of the alien/human cloning experiments, which explains her occasional appearances with the Smoking Man.

As for the serial killer in "Paper Hearts", his knowledge of the details of Samantha's disappearance were explained as a psychic connection to Mulder.

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In the series finale Jeffrey spender testified at Mulders trial that after she was returned from her abduction from the Mulder house in the 70's she was sent to the Spender household where she and Jeffrey grew up together until she died in 1987. Given that the series didn't start til 1993, she was dead all along. For me, personally, this was a huge letdown. Mulder also admits Samantha is dead in I Want To Believe.

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    Welcome to SFF:SE! Yes, in the final episode Spender essentially confirms the explanation given in the Season 7 Episode "Closure". However, I think it is widely known that either Chris Owens (the actor who played Spender) or the script he was reading had transposed two digits in the year --- it should have been 1978. – Praxis Aug 7 '15 at 10:22
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Ever heard of a “walk in” ? Yeah, me either until the season 7 episode "Sein Und Zeit", and the following episode "Closure".

Spoilers to follow.

Samantha Mulder was taken by the Syndicate. She was experimented on for years, her DNA taken and used to create the subsequent clones we saw throughout the series.

We learn in the episode "Closure" from a journal discovered by Mulder that in 1979, after being experimented on for six years at an army base in California, Samantha worked up the courage to escape.

Sadly, she didn’t make it very far and was picked up by two officers who took her to a hospital. Scully was the one who found the police report of a girl matching Samantha’s description being admitted to the hospital. The agents met the nurse who attended to the teenage runaway. The nurse said the girl seemed very sad and at one point the nurse had a vision of this girl dead. (This is an important plot point from the previous episode in which parents had visions of their children being dead right before they mysteriously disappeared.)

While in the hospital the Syndicate tracked down Samantha (the nurse said she remembered the one man whom she asked to put out his cigarette); they were there to take Samantha back to her prison. But, when they went into her room she was gone. Disappeared without a trace.

So what do we learn? Two parents of missing children tell Mulder about “Walk ins.” A type of entity that rescues children doomed to suffer a terrible fate and whisks them off to a type of ethereal realm where they can live forever.

I was always slightly underwhelmed with the big reveal of Samantha’s ultimate fate. It seemed so far from what was always believed happened to her.

It seems these Walk Ins would give the parents a vision of what was to befall their child. Almost like they’re saying, “Look this is what’s going to happen so instead we’re taking your kid to a type of heaven where they can live forever.” So Samantha was ultimately saved from her fate by Walk Ins.

As for the burial ground, those were children that were murdered by Ed Truelove. He had set his sights on a little girl named Amber. She was going to be his next victim but she was saved from this fate by the Walk ins. The other ghostly children seen by Mulder when briefly reuniting with his sister are assumed to all be children taken by Walk ins. Saved by them from experiencing a horrible fate.

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Yes, but nowhere does it specify how she actually died. There's all the preamble about her time on the base, running away, etc - but then she just 'disappeared' again without any real explanation and Mulder finds her soul cavorting around with a bunch of other child ghosts and gets his closure by believing she's dead and 'in a better place'. I always assumed that the fact she was found together with a bunch of other dead kids suggested it was the burial ground of a child serial killer and that she had been one of the victims after running off from the air base.

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    This answer could be improved by editinf quotes and other evidence to the points you make! – TheLethalCarrot Mar 7 '19 at 8:07

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