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Many practical systems are phased-mission systems (PMS), where the mission consists of multiple, consecutive, and non-overlapping phases of operation. An accurate reliability analysis of a PMS must consider the statistical dependencies of component states across phases, as well as dynamics in system configurations, success criteria, and component behavior. In this paper, we propose a method for exact reliability evaluation of arbitrary binary or multi-state PMS consisting of non-identical binary non-repairable elements. The method is invariant to changes in system structure and demand among missions, and takes into account the time-varying and phase-dependent failure rates and associated cumulative damage effects. The proposed method is based on conditional probabilities, and an efficient recursive formula to compute these probabilities based on branch and bound. The main advantage of this method is that it does not require composition of decision diagrams, and can be fully automated. The method is illustrated using both an analytical example, and a numerical example.