As a research tool, virtual environments (VEs) hold immense promise for brain scientists. Yet to fully realize this potential in non-human systems, theoretical and conceptual perspectives must be developed. When selectively coupled to nervous systems, virtual environments can help us better understand the functional architecture of animals’ brains during naturalistic behaviors. While this will no doubt allow us to further our understanding of the neural basis of behavior, there is also an opportunity to uncover the diversity inherent in brain activity and behavior. This is due to two properties of virtual environments: the ability to create sensory illusions, and the ability to dilate space and/or time. These and other potential manipulations will be characterized as the effects of virtuality. In addition, the systems-level outcomes of virtual environment enhanced perception will be discussed in the context of the uncanny valley and other expected relationships between emotional valence, cognition, and training. These effects and their usefulness for brain science will be understood in the context of three types of neurobehavioral phenomena: sensorimotor integration, spatial navigation, and interactivity. For each of these behaviors, a combination of illusory and space/time dilation examples will be reviewed. Once these examples are presented, the implications for improving upon virtual models for more directly inducing the mental phenomena of illusion and space/time dilation will be considered. To conclude, future directions for integrating the use of VEs into a strategy of broader biological inquiry will be presented.