This research provides a comprehensive analysis of the transition pathways towards net-zero emissions in Indonesia's energy sector by 2050, focussing on overcoming the country's fossil fuel dependency. Utilising EnergyPLAN and MultiNode simulations across three scenarios: Nationally Determined Contribution, High Electrification and Moderate Electrification, the paper presents thorough scenario development and cross-sectoral analysis to capture future energy systems from both supply and demand sides. It contributes notably by detailing scenario-specific energy demands, such as industry sector energy efficiency and electric vehicle penetration and introducing a novel modelling approach that segments the Indonesian energy system into five regional systems. Modelling results indicate the necessity of transitioning towards 100 % renewable energy, emphasising the central role of electricity in future energy systems and the importance of regional connectivity in achieving net-zero emissions. Results also reveal that the Moderate Electrification scenario offers a cost-effective route to net-zero emissions by reducing energy demand and fully exploiting renewable energy sources. The paper concludes with policy recommendations to boost energy efficiency, accelerate electrification, initiate interconnected regional energy systems, and leverage carbon capture and storage as a supplementary measure.