Designers and evaluators of immersive virtual reality systems have many ideas concerning how virtual reality can facilitate learning. However, we have little information concerning which of virtual reality's features provide the most leverage for enhancing understanding or how to customize those affordances for different learning environments. In part, this reflects the truly complex nature of learning. Features of a learning environment do not act in isolation; other factors such as the concepts or skills to be learned, individual characteristics, the learning experience, and the interaction experience all play a role in shaping the learning process and its outcomes. Through Project Science Space, we have been trying to identify, use, and evaluate immersive virtual reality's affordances as a means to facilitate the mastery of complex, abstract concepts. In doing so, we are beginning to understand the interplay between virtual reality's features and other important factors in shaping the learning process and learning outcomes for this type of material. In this paper, we present a general model that describes how we think these factors work together and discuss some of the lessons we are learning about virtual reality's affordances in the context of this model for complex conceptual learning.