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Immersive environments such as virtual reality (VR) offer new possibilities for engaging learners in scientific reasoning through embodied and collaborative practices (Lindgren & Johnson-Glenberg, 2013). Yet studying these experiences raises complex questions: How does meaningful collaboration unfold when learners interact in virtual spaces? How do embodied actions—such as gesture, gaze, and movement—shape reasoning across scales in science? In this talk, I will share insights from ongoing work investigating physiological and behavioral synchrony through multimodal methods (Lawrence & Weinberger, 2022) as indicators of joint engagement when pairs interrogate a scientific VR simulation (Lui et al., 2023). These challenges invite us to explore the interplay between cognition, embodiment, and social interaction as mediated by immersive technologies. Drawing on examples from design-based research and emerging multimodal studies of collaborative inquiry in VR, I will highlight tensions and opportunities for measuring and interpreting complex reasoning in immersive worlds. Participants will be invited to discuss implications for research design, data interpretation, and the future of collaborative science learning in immersive environments.