Green hydrogen is an important energy source for replacing fossil fuels for a cleaner transition. While small-scale applications of green hydrogen have proven successful, large-scale nationwide adoption is essential. However, such a change cannot be accomplished overnight. Therefore, this study proposes a staged hydrogen economy scenario for Japan based on the existing energy sources. In this scenario, thermal power generation will be gradually phased out, and the energy shortfall will be compensated by increasing the penetration of renewables and energy storage. Hydrogen and ammonia serve as short- and long-term energy storage solutions, respectively. A data-driven model combining heuristics and optimization methods was designed to address optimal planning and sizing problems. The results show that it is feasible to achieve a 20 % reduction in thermal power by replacing it with renewable energy and hydrogen or ammonia. The lowest levelized cost of electricity (LCOE) in Tokyo (Kanto district) is 0.072 USD·kWh−1, which is comparable to the baseline scenario (using fossil fuels). Hydrogen and ammonia are effective in reducing the LCOE and addressing the mismatch between supply and demand. A higher reduction in thermal power requires further technological and policy support. According to the sensitivity analysis, hydrogen prices and carbon taxes have a high potential to advance the hydrogen economy scenario in the future.