Science considers itself the ultimate authority on empirical knowledge, but dismisses many modes of empiricism that do not fit neatly into its methods. Development in scientific directions means that those neglected areas become a "Near Frontier" of underdeveloped modes of knowledge. This leads to a Dark Age in those realms.
Science is a method of inquiry, and only that. It is not the only path to knowledge. It is not the method of inquiry best suited to certain forms of knowledge. Other methods are not only atrophied during the reign of science, they are actively ridiculed as worse than useless.
What methods would those be?
- Personal introspection, in the vein of Jungian Analysis and others, where one is at once the observer, the subject, and the device of measurement
- Hyperscription (Sigil Magick) and other psychic practices, where the result of an input is determined by more than simply its material components, subject to unwitting interference by a researcher
- The study of Meta-logical planes of existence, such as that of the Samsari
To make this idea shine in a narrative, science would need to reach the extent of its capabilities with a hidebound insistence that there is no more to be learned. At this point, the church of science might become an actual church.