I Made You a Whole Person" . . . Mulder turned around in exasperation as Scully shut the door behind her.
"What does it take? For this thing to come up and bite you on the ass?" He laughed lightly in disbelief at her refusal to accept the truth. "I saw these creatures. I saw them burst to life. You woulda seen them too, but you were infected with that virus," gesturing to his shoulder, he continued, "but you were passed out over my shoulder."
Scully shook her head slightly, "Mulder, I know what you did. I know what happened to me, but without ignoring the science, I can't --" she broke off and then abruptly she cried, "listen, Mulder," and she reached out, firmly grasping his hand. "You told me that my science kept you honest . . . that it made you question your assumptions," she said, reminding him of his declaration in his apartment hallway, "that by it, I made you a whole person."
Mulder looked searchingly into her eyes, seeing the truth and the honesty there.
"If I change now," Scully continued, "I . . . " she paused, searching herself, for the words to make him see, "it wouldn't be right or honest."
"I'm talking about extraterrestrial life alive on this planet in our lifetime. Forces that dwarf and proceed all human history."
Her gaze dropped slightly and then she met his eyes as he finished softly, "I'm sorry, Scully, this time, your science is wrong."
And then he let go of her hand, walking away as she watched him go.