In 1875 Balfour Stewart and Peter Guthrie Tait published The Unseen Universe, an odd book that attempted to combat materialism by using the newly formulated law of the conservation of energy to rationally explain supernatural ideas like miraculous happenings, the immortality of the soul, Christ’s Incarnation, angels, and more. Stewart and Tait accounted for these supernatural ideas and addressed the worrying prospect of the heat death of the universe by proposing a second, unseen universe that was tied to the seen universe through bonds of energy transference. The book represents an attempt at the reconciliation of several contradictory and complimentary systems of understanding into a new unified synthesis. This paper will present a brief introduction to and systems-based analysis of this odd work of natural philosophy, placing it in its scientific, cultural, and philosophical context, and by doing so will provide a glimpse into the broader world of competing systems of understanding in Victorian science, rife as it was with philosophical non-simultaneity and intellectual ferment. By taking a systems-analytical approach to a complex text like this we can gain insight into the ways in which competing systems of understanding interact in times of intellectual change.