Dana Scully

Context: Throughout the series, her Catholic faith served as a cornerstone, although a contradiction to her otherwise rigid skepticism of the paranormal. Due to her career in science and medicine, she drifted from her Catholic Christian upbringing but remained somewhat entrenched in her religious beliefs. Scully almost always wears a gold cross necklace, given to her by her mother as a Christmas present when she was fifteen. When she was abducted by Duane Barry, a self-proclaimed alien abductee, it was the only item left behind in Barry's getaway car. Mulder wore it as a talisman of her until Scully miraculously reappeared in a Washington, D.C. hospital. After she recovered from the trauma of her abduction, he returned the cross to her. The abduction visibly tested the limits of her faith -- Mulder believes that Scully was taken aboard an alien spaceship and was subjected to tests. However, because of Scully's skepticism, she believes she was kidnapped by men and subjected to tests, not aliens. She believes she could have been brought there by Barry, and she began to exhibit symptoms of post-traumatic stress disorder on a case involving a murdering fetishist named Donnie Pfaster. This psychological re-victimization continued after Pfaster escaped from prison five years later and again attempted to kill her in her home, ending only after she fatally shot him. She struggled with what motivated her actions to kill Pfaster, and questioned whether it was God compelling her to kill him, or "something else." Sometime after her recovery from cancer, Scully began to regularly attend Mass again. At the request of Father McCue, Scully got involved in a case concerning a paraplegic girl who was found dead in a kneeling position with her palms outstretched and eye sockets charred. After Scully discovered the girl was part of a set of quadruplets and two more were murdered, Father McCue shared with her the story of the seraphim and the nephilim, which Scully interpreted as a possible explanation for the deformations and deaths of the girls. Scully continued to have visions of Emily, and when the last girl died, Scully believed she was returning the girl to God. Upon her return to Washington D.C., she went to confession to gain peace of mind and acceptance for Emily's death. In confession she regretted her decision of letting the girl go. This suggests Scully had doubts about her faith. In the sixth season episode "Milagro", Agent Scully's vulnerability is exposed. In this episode, the murderer takes the victim's heart out. The suspect, a writer named Phillip Padgett, has a particular interest in Scully and is fascinated by her beauty and personality. When she goes to a church to observe a painting, the writer is there and talks to her about the Sacred Heart of Jesus. During the conversation he says she visits the church because she likes art, but not as place of worship. Scully doesn't say otherwise and later she says to Agent Mulder the writer told her her life story. All this suggests that Scully isn't a devout Roman Catholic, although she attempted to approach again the Catholic community and the Catholic faith to which she was devout in her youth, after handling the strange case presented in "Revelations" and also after dealing with life-threatening cancer during the fourth season. CANNOTANSWER

Question: Why did Mulder believe that Scully was taken aboard an alien spaceship and was subjected to tests?
Answer: However, because of Scully's skepticism, she believes she was kidnapped by men and subjected to tests, not aliens.