This study examined the comparative effects of two instructional models under Contextualized Adaptive Differentiated Instruction (CADi)—the Adaptive Station Rotation Model (ASRM) and the Four-Phase Gradual Release of Responsibility (GRR) Model—on the learning autonomy and critical-thinking skills of Grade 9 science learners. Grounded in Constructivism, Self-Determination Theory, and Differentiated Instruction, the study addressed persistent concerns regarding learner dependence on teacher-directed instruction and limited higher-order thinking in science education. A quasi-experimental non-equivalent groups posttest-only design was employed. Two intact Grade 9 classes from Cuyab Integrated National High School during Academic Year 2025–2026 were selected through cluster sampling and assigned to either the ASRM or GRR instructional condition. Both groups received instruction on impulse, momentum, and collisionrelated phenomena over approximately four weeks using contextualized and differentiated learning experiences. Learning autonomy was measured through an adapted Learning Autonomy Questionnaire based on the framework of Nguyen and Habók, while critical-thinking skills were assessed using a contextually adapted instrument derived from the Physics Lab Inventory of Critical Thinking. Descriptive and inferential statistics were utilized to analyze posttest results. The study aimed to generate empirical evidence on the implementation of CADi in public secondary science classrooms and determine whether differences exist in learning autonomy and critical-thinking skills between the two instructional models. Findings may contribute to the design of adaptive, learner-centered, and contextually responsive science instruction.