There is no reason to keep her in protective custody, Mulder.
Later, Scully shines the flashlight in Mulder's face.
An oncoming car honks and crashes into Mulder, sending him flying up into the windshield, which cracks.
They are watching the original videotape of MULDER's regression hypnosis about Samantha.
The physical X Files are a charred mess, and Mulder is trying to recreate the documents.