Many episodes hint that she was abducted and cloned for a plan of putting alien/human hybrids on earth for some kind of secret plan to colonize them. Mulders work is fueled by the assumption that his sister is still alive. and every x-files brings him closer to the truth or the lie. In "mirricle man" a faith healer tells mulder that she may still be alive. And in "duane barry" a man who said he was abducted saw children being given painful "tests". Several times in the past few episodes has mulder seen a version of his sister. in "colony" he saw a grown up version of samantha only to findout that it was a clone. In "herrenvolk" mulder went to a bee field and saw many young clones of his sister working in a field with bees. In "demons" mulder is put under a treatment where he remembers repressed memories and see's his sister being taken away.
FAITH TO KEEP LOOKING