Open-ended scenario questions encourage undergraduate animal physiology students to develop critical thinking and creative problem-solving skills as they practice applying course material to real-world contexts. Because each student can take their own unique approach to answering the question, when responses are posted to a group discussion board, students are exposed to different approaches to solving the problem, leading to a more well-rounded understanding of the associated physiological concepts. With the increased availability and student use of generative AI tools, over the course of several semesters, responses became more uniform, with students showing a poorer understanding of the underlying physiological principles on summative assessments. This teaching intervention used a series of three scaffolded assignments throughout the semester to leverage students’ interest in incorporating generative AI into their coursework. The goal was to encourage the development of a thoughtful approach to AI use in these scenario-based assignments, without sacrificing their understanding of the course material. The three assignments followed a progressive increase in student agency over how they used AI: the first relied exclusively on instructor-provided prompts, the second required that students design their own follow-up prompts to optimize the initial response, and the third allowed students to develop their own approach to answering the question, using AI entirely at their discretion. Each discussion required peer-to-peer engagement through posting responses and their AI approach to a discussion board, so students could compare how different AI use strategies were reflected in the generated responses. To deepen connections between AI-generated text and course materials, students created original graphics illustrating the physiological mechanisms they described in their responses. Finally, students reflected on how AI supported their learning and understanding of physiological concepts. This progression was designed to promote critical engagement with generative AI while strengthening mastery of physiology through creativity, collaboration, and reflection.