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Undergraduate students ( N = 82) learned about microbiology with Crystal Island, a game-based learning environment (GBLE), which required participants to interact with instructional materials (i.e., books and research articles, non-player character [NPC] dialogue, posters) spread throughout the game. Participants were randomly assigned to one of two conditions: full agency , where they had complete control over their actions, and partial agency , where they were required to complete an ordered play-through of Crystal Island. As participants learned with Crystal Island, log-file and eye-tracking time series data were collected to pinpoint instances when participants interacted with instructional materials. Hierarchical linear growth models indicated relationships between eye gaze dwell time and (1) the type of representation a learner gathered information from (i.e., large sections of text, poster, or dialogue); (2) the ability of the learner to distinguish relevant from irrelevant information; (3) learning gains; and (4) agency. Auto-recurrence quantification analysis (aRQA) revealed the degree to which repetitive sequences of interactions with instructional material were random or predictable. Through hierarchical modeling, analyses suggested that greater dwell times and learning gains were associated with more predictable sequences of interaction with instructional materials. Results from hierarchical clustering found that participants with restricted agency and more recurrent action sequences had greater learning gains. Implications are provided for how learning unfolds over learners' time in game using a non-linear dynamical systems analysis and the extent to which it can be supported within GBLEs to design advanced learning technologies to scaffold self-regulation during game play.