In Chap. 2, we briefly introduce essential system-scientific tools for modeling, analyzing, and mitigating cognitive vulnerabilities and cognitive attacks. Decision theory in Sect. 2.1 provides a scientific foundation of making decisions for single agents with different rationality levels under stochastic environments. Game theory is introduced in Sect. 2.2 to model the strategic interactions among multiple agents under several basic game settings and their associated Nash Equilibrium (NE) solution concepts. To address the challenges of incomplete information in decision-making and game modeling, we present two learning schemes in Sect. 2.3. These tools provide a system-scientific perspective to evaluate and reduce uncertainty in HCPSs, as illustrated by the blue and red lines in Fig. 2.1, respectively. We refer the readers to the notes at the end of each section for recent advances and relevant references.