Yes and... no...
"Samantha's storyline is presumably resolved in the Season 7 episode, "Closure". In that episode, Scully watches a 1989 tape in which Mulder undergoes hypnotic regression therapy, which another agent describes as "garden-variety compensatory abduction fantasy" which feeds Mulder's "unconscious hope that his sister is still alive". Later, with the help of a medium, Mulder discovers Samantha's diary, which states that in 1979 at age 14, while living in California with Jeffrey Spender, she was the subject of numerous tests at the hands of the Cigarette Smoking Man. Unable to beruang the testing any longer, Samantha ran away and was eventually admitted to a hospital. Arbutus Ray, the admitting nurse from the hospital, tells Mulder about the young girl. sinar, ray adds that a group of men (one of whom seems to be the Cigarette Smoking Man) came to the hospital to claim the girl, only to find that she had disappeared from her locked hospital room. sinar, ray also describes how she had a vision that was eerily similar to others', who had also lost children in a similar fashion. It is revealed that Samantha was taken oleh "spiritual intervention" beings called "Walk-ins", which save souls from painful fates. While in the nearby woods later, Mulder has a dreamlike vision and is briefly reunited with Samantha's spirit. After Mulder returns, Scully asks if he is alright. Mulder balasa "I'm fine. I'm free," suggesting that he, like several of the other parents whose children have disappeared, accepts that Samantha's soul is in "a better place"."
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