Critical thinking is widely recognized as essential for education and professional practice, particularly as artificial intelligence (AI) transforms engineering education and work. This paper examines the relationship between AI and critical thinking in engineering through Mejía's three-sphere framework: intelligent tool use, comparative analysis of methods, and socio-technical impacts. We propose a research methodology to evaluate how generative AI can enhance critical thinking capabilities among engineering students. The study employs a mixed-methods approach across two engineering courses, with a framework that focuses on engineering-specific cognitive processes while integrating technical and sociotechnical considerations throughout the engineering lifecycle.