AI has quietly rewritten the rules of research, yet many research methods courses still operate as if it hasn’t. In this session, we share the redesign of an interdisciplinary research methods course that proposes to teach with and about AI by design, not by accident. Moving beyond AI policing or unstructured use, we introduce a practical pedagogical framework that scaffolds student thinking, makes learning visible, and integrates critical AI literacy into core research practices. Using an online research methods course redesign as a case study, we'll explore how to structure AI as a "thinking partner," "practice partner," and "support partner." These are roles that scaffold learning rather than replace it. We'll share specific strategies for designing AI-transparent assessments that make student thinking visible and demonstrate authentic research competency. Leave with actionable approaches for redesigning your own courses to build both disciplinary skills and critical AI literacy simultaneously.