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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 they stated this was a screwup by show creators and never addressed for real – DVK Mar 7 '12 at 16:56
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

2 Answers 2

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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 at 10:22

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