This book presents a series of revised papers selected from the Second MICCAI Student Board Workshop, EMERGE 2025, Held in Conjunction with MICCAI 2025, Daejeon, South Korea, September 23, 2025, Proceedings. The 13 full papers presented in this book were carefully reviewed and selected from 19 submissions. These papers were organized in the following topical sections: Foundation Models and Generalization in Medical AI; Representation Learning for Detection and Diagnosis; Signals, Bias, and Structure in Medical Data; Poster Presentations.