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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 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
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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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