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The goal of this paper is to provide a mathematical threat modeling methodology and a threat risk assessment tool that may assist security consultants at assessing the security risks in their protected systems/plants, nuclear power plants and stores of hazardous substances: explosive atmospheres and flammable and combustible gases and liquids, and so forth, and at building an appropriate risk mitigation policy. The probability of a penetration into the protected objects is estimated by combining the probability of the penetration by overcoming the security barriers with a vulnerability model. On the basis of the topographical placement of the protected objects, their security features, and the probability of the penetration, we propose a model of risk mitigation and effective decision making.