The subtitle I Want to Believe well captures the subplot, of Catholics feeling alienated by pedophiles in the priesthood, taken advantage of by those they've been raised to trust.
Scully feels this sense of betrayal especially intensely, given problems with her bureaucracy at work, a somewhat dreary Catholic hospital.
Her suspicions of Mulder's bull-headed dogmatism, fascination with the dark side, return to the surface. How gullible does he expect us to be? The FBI is wondering the same thing, always has.
Predictably, Mulder thinks the "psychic priest" is truly psychic, not just leading the FBI on a wild goose chance in an effort to cover up his complicity in as yet unconfessed crimes -- still involving an altar boy, or part of one.
The gothic horror is tinged with disturbing enough realism to remind us of where medical science sometimes takes us. The ethical issues may be intense, the trade-offs uncomfortable, so we really do need a strong faith in a wisdom deeper than our own. Scully's suffering is therefore as believable as the ghoulish Russians are ridiculous.
The note of self-spoof is unmistakable, keeping X-Files from taking itself too seriously, a hallmark of this literature.