Global energy systems are changing rapidly. This energy transition complicates the use of traditional policy analysis methods. However, proper policy analysis and design is essential in managing the transition. This thesis takes an interdisciplinary approach to analyze three policy issues for the Swiss energy transition, making contributions to policy analysis methodology, sustainability transitions, external governance, as well practical contributions to the governance of the Swiss electricity sector. The first essay analyzes the impact of the timing uncertainty of the nuclear phase-out. In 2011, the Swiss government decided to phase-out nuclear power but allow the plants to remain online for as long as they can be operated safely, leaving their final operating date uncertain. This decision is analyzed using a system dynamics (SD) simulation model. The results show that the timing uncertainty does not impact the market development or security of supply. However, delaying the nuclear phase-out can have significant advantages for greenhouse gas emissions and security of supply. In all simulated scenarios, Switzerland becomes more dependent on electricity imports. The second essay analyzes the governance of energy relations between Switzerland and the European Union (EU). Switzerland and the EU have highly interdependent electricity systems, but there is a relatively low level of policy alignment and no formal Swiss-EU electricity agreement. The historical developments in Swiss-EU energy policy are reconstructed through a series of interviews and analyzed using an external governance theoretical framework. Gradual harmonization of EU electricity markets and certain key events have driven Switzerland's exclusion from EU network governance processes, leading to more hierarchy, reducing Swiss influence on legislative processes, and deteriorating trading conditions. The negotiations for an electricity agreement present an opportunity to reverse this trend, but the future of Swiss-EU bilateralism remains politically uncertain and will depend on general relations more than electricity sectoral dynamics. The third essay analyzes the Swiss proposal for a strategic energy reserve: a novel policy to increase security of supply in winter, potentially at risk due to the growing import dependency and deteriorating Swiss-EU relations. The policy incentivizes storage operators to keep a minimum amount of energy in reserve, for use in scarcity periods. A new hybrid simulation model is created, combining system dynamics and agent-based modeling. The results show that a strategic energy reserve can improve short-term, but not long-term security of supply. It will likely be cost-ineffective and risks inducing artificial scarcity periods. Any implementation should be done on a dynamic, ad hoc basis, conditional on a short-term adequacy assessment to minimize the costs while increasing the benefits. The thesis makes several important contributions. It contributes to hybrid and simulation modeling for policy analysis and transitions research. The model offers novel tools for combining short- and long-term market dynamics, opportunity cost bidding, and strategic energy reserves. The findings of each essay are directly relevant for policymakers to inform their decisions about the analyzed policy issues. Finally, the thesis contributes to the theories of sustainability transitions and external governance.