In the 2005 NSTA monograph Exemplary Science in Grades 9–12: Standards-Based Success Stories, the authors present and discussed student inquiry at the Illinois Mathematics and Science Academy (IMSA) (Scheppler et al. 2005). This monograph focused on the on-campus portion of the SIR program for STEM investigations. Evaluation and evolution of the SIR program has led them to consolidate and standardize the experiences for students pursuing work both on campus and off campus. What they have learned from having students conduct inquiry investigations and the rethinking of their science program led them to design, develop, and implement a required core science course for all of their incoming sophomore students. This course helps prepare students for their own independent investigations and supports their development with respect to various habits of mind important to science. This chapter discusses the course, Methods in Scientific Inquiry (MSI), how knowledge from this course has transferred into their science elective program, and how it has improved the quality of SIR investigations that their students conduct. Also included is a discussion of their long-term successes with IMSA graduates. This free selection includes the Table of Contents and Index.