Submarines face an ongoing (technical) battle to improve the operational effectiveness by increasing the submerged endurance and range. Currently, diesel-electric submarines mostly implement traditional lead-acid batteries as the main source of power when submerged. Installing more modern options, like lithium-ion batteries, on new or refitted diesel-electric submarines can increase the submerged range with at least a factor 2. Additionally, lithium-ion batteries require less maintenance and provide a relatively longer life expectancy compared to lead-acid batteries. However, lithium-ion batteries can develop a thermal runaway: a process which exponentially generates heat, leading to the risk of an explosion and fire. Additionally, the gasses formed in the thermal runaway process are toxic, corrosive and flammable. Therefore, research is required into preventing a thermal runaway of lithium-ion batteries and mitigating the risks caused by a thermal runaway on submarines.\\ This paper investigates: a) the required cooling to prevent thermal runaway or limit it to a single cell, and, b) measures to protect crew and submarine against the consequences of a thermal runaway of lithium-ion batteries. The paper proposes a novel thermal runaway model based on a heat development model in literature and extends it with a model that establishes the quantity of combustible gasses. This model is verified with results of two standard tests from literature and subsequently used to investigate the process of thermal runaway under a number of scenarios. The modelling results calculate the required cooling capacity to prevent a thermal runaway or limit it to a single cell and investigate the effectiveness of three fire distinguishing systems in limiting the consequences of a thermal runaway and preventing cell-to-cell or module-to-module propagation. The conceptual investigation and discussion of the results do not provide a complete philosophy or validated design procedure but the work clearly demonstrates that a) the risk of thermal runaway can be significantly reduced by a thorough design of battery modules and the associated cooling system and that b) the consequences of a thermal runaway can be mitigated by a well designed fire extinguishing , for which foam and compressed are foam appear to provide promising results under the studies assumptions and that c) the risks of thermal runaway can be strongly reduced by installing a well designed gas drain system. In order to validate the results of this first conceptual investigation, further work is required to provide more detail to the evaluated protection measures and system designs, validate the thermal runaway models with physical destructive tests and validate the ultimate battery and protection systems, first with the proposed models and finally, after optimising these designs, with destructive tests of the proposed systems.