Thermal runaway and subsequent fire in Li-ion cells and battery packs is of much concern in the safety of practical electrochemical energy storage systems. While much of the past work in this direction has focused on single cells or small packs, there is a relative lack of understanding of thermal runaway related fire and fire suppression strategies for large-scale systems, for example in storage and transportation of Li-ion cells. This work presents a simulations-based investigation of strategies for effective prevention and suppression of thermal runaway propagation and resulting fire in pallets containing a large number of Li-ion cells. The impact of location, orientation and flowrate in sprinklers supplying a liquid coolant is quantitatively investigated. It is shown that a minimum flowrate is needed for effective fire containment, beyond which, additional flowrate does not offer much incremental benefit. The orientation of sprinklers with respect to the trigger pallet undergoing thermal runaway is found to strongly impact the effectiveness of fire suppression. Fire suppression in the case of vertically stacked pallets is also investigated. Interesting synergistic effects involving a combination of liquid coolant along with one or more suppressant gases is demonstrated. The key output of this work is a computational model that quantitatively predicts the effectiveness of fire suppression techniques for battery transportation and storage. Results presented here offer a fundamental understanding of an important practical problem in battery-based energy storage. Results may form the basis of design and optimization to ensure the safety of large-scale storage and transportation of Li-ion cells.