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Experiences in immersive 3D virtual reality (VR) are more presence-inducing, and so it may be tempting to claim that content will be learned better in VR. This randomized control trial study on natural selection challenges that assumption. This study answers the question of whether learning STEM in an immersive 3D VR environment is always superior to learning via a 2D monitor (PC). This is a 2 × 2 × 3 design. The first factor is platform immersivity (low = 2D PC, or high = 3D VR), the second factor is level of embodiment (lower = watching playback video, or higher = using mouse/controller to agentically manipulate content), and the third factor is test time (pretest, posttest, and follow-up). There was a significant main effect for embodiment, the high embodied and agentic groups learned the most. There was not a main effect for platform, because the participants in the low embodied VR group performed significantly worse than the three other groups. Although, the one high embodied, VR group learned and retained the most knowledge. A path-analysis revealed that the effect of platform was significantly mediated by presence, agency, and engagement. The smaller learning gain in the low embodied VR condition suggests that participants come to the immersive VR experience with expectations about agency and control of the virtual content, and when those expectations were not met, the disconnect was deleterious for learning. More agentic and interactive control of manipulable virtual content is encouraged. Design is critical, and platform is not destiny.