Bacillus anthracis spores have shown extreme resistance to heat treatment methods. Various novel ideas have emerged including the use of thermite reactions for the de-activation of bacterial spores, focusing on the anthrax forming spore Bacillus anthracis. The basis of de-activation is dependent on the heat transfer to the spore and chemical interaction with the halogen gas. The objective of this work was to observe the mechanisms of de-activation as related to the thermal and halogen gas effect on the spore. Research focused on the specific roles of the heat transfer and the combination of heat and halogen gas. Results showed heat transfer in the spore greatly enhanced the effectiveness of the halogen gasses in the deactivation process. The observed results strengthen the hypothesis that the heat transfer affects the permeability of the bacterial spores, enabling the halogen gas to deactivate the spores. This novel observation leads to further studies in the combustion properties of thermites. Results from this study suggest that thermite formulations with increased heat of reaction will increase the thermal wave promoting spore neutralization.