The Indonesian government has set a target to increase new and renewable energy sources in the energy mix by 23% in 2030 and 31% in 2050, which are to be met by investing in hydropower and geothermal energy capacity mainly. However, Indonesia has abundant other renewable energy potentials, which are largely untapped. The Java-Madura-Bali (Jamali) system is Indonesia's largest electricity system. Integration of variable renewable energy resources requires flexibility options such as grid expansion and short- and long-term electricity storage. This research aims to fill the knowledge gap in the literature on the effect that different carbon emission reduction limits have on the Jamali power system design in 2050. This was done by studying the potential of various promising renewable energy technologies (solar photovoltaics, on- and offshore wind, Ocean Thermal Energy Conversion (OTEC), geothermal and hydropower) in combination with short- and long-term storage (lithium-ion batteries and hydrogen storage) and grid expansions to mitigate renewable variability. For this purpose a techno-economic model was developed that optimizes operation and capacities of generation, storage and network simultaneously. The model simulates the system dynamics in the Jamali system in 2050 and was implemented in Python for Power System Analysis (PyPSA). It was found that there is an exponential relationship between system costs and carbon emission reductions in the Jamali power system. Additionally, only moderate system cost increases were found up to 80% emission reductions compared to the reference scenario with no emission mitigation efforts. At higher carbon reduction scenarios the solar capacities reach their maximum installable capacities. As a result, system cost increase exponentially due to the need for OTEC and offshore wind capacities. The high costs increases by offshore wind can be explained by the uniform costs and coarse resolution of the model. In low carbon scenarios high battery capacities were found and network expansion is limited. It is concluded that the Jamali network cannot smooth the variability of wind throughout the power system, therefore, without storage capacities the system cost almost double. On the other hand, the network remains important to transport electricity from rich renewable regions to large demand centers. Based on the results three recommendations were proposed related to the reconsideration of the energy targets for 2050, strategy to achieve the targets and present policies.