This paper presents a novel Fault Adaptive Mission Planning (FAMP) framework for complex systems aimed at increasing useful-life and reducing downtime through condition-based decision-making. A hallmark of complex systems is that they typically have access to multiple mission plans that allow their mission objectives to be accomplished in a variety of ways. In hopes of exploiting this characteristic, FAMP is the process of increasing a system's useful-lifespan by first determining how each potential mission plan affects the system's degradation differently, and then by implementing a planning strategy that utilizes this information to repeatedly recalculate a new mission plan as the system degrades. Fault-augmented physics models identify how component degradation will affect the system's current and future performance for a given mission plan. Then, at various degradation-based thresholds, new mission plans are installed such that whenever possible, the healthiest components are used more, or in different ways, than the more degraded components. This process promotes balanced degradation, preventing useful-life from being wasted and reducing downtime through synchronized maintenance schedules. This work expands the prognostics and health management paradigm by enabling life extension and maintenance reduction through real-time FAMP.