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?