The dynamic autonomy resulting from control mode transitions in the Maritime Autonomous Surface Ships (MASS) poses a significant risk to its navigation safety. While Systems-Theoretic Process Analysis (STPA) has proven effective in the hazard identification of autonomous ships, the safety challenges inherent in the dynamic autonomy of MASS with seafarers onboard controlled by three possible controllers have not been addressed much. This study proposes a three-phase framework that combines STPA, state machines and Sequentially Timed Events Plotting (STEP) diagram aiming at identifying failure scenarios in the transition process. Findings from a case study highlight the need for such a framework to understand the triggering events for mode transition, the transition process, how transition failure may occur, and refine safety constraints to ensure smooth and safe transitions. The results lay the groundwork for future research into test case generation methods that focus on these identified transition failure scenarios, intending to ensure safe and secure navigation for the progressive introduction of MASS.