Multiple Sclerosis (MS) is a chronic autoimmune disease affecting the central nervous system, with over 2.9 million cases globally. Magnetic Resonance Imaging (MRI) is essential for diagnosing and monitoring MS, focusing on lesion detection and progression. This project aims to develop an AI framework to automatically analyse MRI sequences, segmenting and analysing lesion progression over time. Additionally, it seeks to optimise MRI scan timing, balancing new lesion detection with treatment efficacy. Furthermore, the project seeks to enhance clinical trust and understanding by incorporating Explainable AI (XAI) techniques.