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During the seventh season, Mulder eventually discovers the truth about his sister.

Samantha was abducted ( either by the alien colonists or the government conspirators ), and various tests were performed on her.

She was then returned to The Smoking Man to live out her life under his supervision, all the while undergoing additional tests.

She was unable to bear the testing any longer so she ran away from her home and was eventually admitted to a nearby hospital, where she disappeared from her locked room.

It is revealed that Samantha was taken by " spiritual intervention ", with the help of beings called " Walk-ins ".

Mulder is briefly reunited with Samantha's spirit.