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This study examined the effect of learner autonomy on proportional learning gains (PLGs) from pretest-posttest scores and affective states while reading to solve a mysterious illness within a game-based learning environment (GBLE), CRYSTAL ISLAND. Undergraduates (n=85) were randomly assigned to two conditions varying in autonomy. Results indicated those with limited autonomy over their actions demonstrated greater PLGs than those with full autonomy. Affective states (joy, anger, confusion, and frustration) differed between conditions where learners with full autonomy exhibited greater evidence of these states based on facial expressions video analysis during learning. These states differed where, from greatest to least evidence scores, anger, confusion, frustration, and joy are displayed by learners while reading, with no differences in their occurrence frequency.