The Matrix is the symbolic representation of data and data pathways in the virtual reality in which Case engages. By taking hypermedia one step further into the future in this manner, Gibson raises a question that needs to be addressed by intermediate systems. First, how should information be represented, or put another way, what does data look like? In Case's virtual reality, there are no numbers to crunch, no graphs to read. In this reality the conscious mind and the body are separated by the device, and the mind is allowed unparalleled freedom. One notes, though, that the representation, while allowing this freedom, essentially takes place through the visual and auditory modalities. The reality is represented in a way that corresponds to input that the mind expects.
Therefore, to Case, reality is represented in a three-dimensional network of data highways, where computers are large nodes where network lines converge. This representation seems designed to alleviate any feeling of disorientation that other less "realistic" (read "expectable") representations might cause. Because virtual visual, auditory, and kinesthetic sensory input is analogous to real-world input, Case feels as comfortable in the virtual reality as he does walking around, perhaps more so.
Gibson nicely counterpoints this virtual experience with Case's experience of weightlessness in space, which he finds an "unnatural" environment. When Case boosts into this reality, he experiences what Gibson terms Space Adaptation Syndrome, or SAS. Despite the fact that space is real -- it has an objectivel;y verifiable existence outside his mind -- the weightless environment is much less like the real world that Case grew up in than is virtual reality.