This dissertation presents a set of analytical tools developed to investigate the energy system transition using a systems approach. The cases explored range from Kosovo, a country on the verge of new electricity supply investments, and future energy pathways to an analytical investigation of innovation in battery storage systems that could unlock the environmental and health benefits of intermittent renewable energy sources such as solar and wind technologies. The analytical tools compare existing metrics such as levelized cost of electricity with new metrics such as a two-factor learning curve of deployment and innovation and trace metal content of coal per final kWh of electricity delivered and energy return on investment of distributed energy systems.Chapter 1 investigates the case of Kosovo and introduces an analytic framework to analyze electricity costs and environmental impacts of future electricity options. The scheduled decommissioning of the Kosovo A coal-fired power plant provides an opportunity to investigate the changing cost of alternative energy options available in Kosovo for new energy infrastructure. I find that a range of investment pathways from international financial institutions and donor groups could meet the same projected electricity demand at a lower cost than building a new 600 MW coal fired power plant. The options include energy efficiency measures, combinations of solar PV, wind, hydropower, biomass, and the introduction of natural gas. The results indicate that financing a new coal plant is the most expensive pathway to meet future electricity demand in Kosovo.Chapter 2 utilizes the analytic framework developed to estimate the cost of future electricity pathways and uses green chemistry and public health risk assessment to estimate trace metal content of coal and investigate the air-pollution-related-health risks of lignite coal in Kosovo. By utilizing ICP-MS, I sample lignite coal for trace metal content and develop a risk model to assess future health impacts of air pollution from the electricity options explored in Chapter 1. I find significant trace metal content normalized per kWh of final electricity delivered. I estimate that Kosovo could avoid 2300 premature deaths by 2030 when introducing energy efficiency and solar PV backed up by natural gas. The framework highlights that often multi-lateral development banks do not account for all health risks before guaranteeing loans on new electricity projects. The interest in finding sustainable options to balance the load of intermittent renewable energy options in Kosovo motivates further analysis to understand how battery storage technologies have developed over time in terms of performance and cost.Chapter 3 examines the dramatically falling cost of battery storage options. I develop a two- factor technological learning curve model that integrates the value of investment in materials innovation and technology deployment over time from an empirical dataset covering battery storage technology. I find and chart a viable path to dispatchable $1/W solar with $100/kWh battery storage that enables combinations of solar, wind, and storage to compete directly with fossil fuel-based electricity options. I highlight the co-evolutionary nature of the cost reductions of battery storage technologies and suggest the relative importance of sustained investment and integration of R&D and deployment to develop innovative low-carbon combined solar, storage, and wind systems.Chapter 4 highlights the changing energy return on investment of energy technologies by investigating a case in Thailand where distributed solar, mini-hydro, and battery storage mini- grids are becoming an attractive investment and serve as core options to meet growing demand for electricity. I compare the net energy return on investment (EROI) of mini-hydropower, solar PV, and battery storage. This study represents a direct application of the opportunities for battery storage technologies to enable cost-competitive mini-grids in Thailand and around the world.The dissertation highlights different plans, designs, and future management of cost-effective, sustainable, and healthy electricity systems for a clean energy transition worldwide. The analytical tools presented combine to integrate traditional economic, environmental, and health metrics into energy systems planning and innovation. By integrating these interconnected systems, it becomes possible to enable cleaner and more sustainable energy transitions.